diff --git a/DESCRIPTION b/DESCRIPTION
index c9c635d40..55450e741 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,7 +33,6 @@ Imports:
     glue,
     htmltools,
     htmlwidgets,
-    logger,
     magrittr,
     PKNCA (>= 0.12.1),
     plotly (>= 4.11.0),
diff --git a/NAMESPACE b/NAMESPACE
index 29d1b2d67..c8fdc9788 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -140,7 +140,7 @@ importFrom(glue,glue)
 importFrom(grid,convertUnit)
 importFrom(htmltools,tags)
 importFrom(htmlwidgets,onRender)
-importFrom(logger,log_info)
+
 importFrom(magrittr,`%>%`)
 importFrom(plotly,add_lines)
 importFrom(plotly,add_trace)
diff --git a/R/imports-shiny.R b/R/imports-shiny.R
index 119a2bfa7..2f6e36b92 100644
--- a/R/imports-shiny.R
+++ b/R/imports-shiny.R
@@ -7,7 +7,6 @@
 #' @importFrom bslib page_sidebar
 #' @importFrom htmltools tags
 #' @importFrom htmlwidgets onRender
-#' @importFrom logger log_info
 #' @importFrom reactable reactable
 #' @importFrom reactable.extras reactable_extras_dependency
 #' @importFrom shiny runApp
diff --git a/inst/shiny/app.R b/inst/shiny/app.R
index 55e5c4c96..26a8bb642 100644
--- a/inst/shiny/app.R
+++ b/inst/shiny/app.R
@@ -3,7 +3,6 @@ require(aNCA)
 require(bslib)
 require(dplyr)
 require(htmlwidgets)
-require(logger)
 require(formatters)
 require(magrittr)
 require(plotly)
diff --git a/inst/shiny/functions/logging.R b/inst/shiny/functions/logging.R
new file mode 100644
index 000000000..ce29dedbc
--- /dev/null
+++ b/inst/shiny/functions/logging.R
@@ -0,0 +1,84 @@
+# Lightweight logging system for the aNCA Shiny app.
+#
+# Replaces the `logger` package with console-only output and in-memory
+# log capture for ZIP export. Supports glue-style interpolation and
+# paste-style multi-argument calls.
+#
+# Log levels: TRACE < DEBUG < INFO < SUCCESS < WARN < ERROR
+# Default threshold: INFO (configurable via aNCA_LOG_LEVEL env var).
+#
+# The log captures application-level events only — not raw R console
+# output. Warnings and errors from third-party packages appear only
+# when explicitly caught by tryCatch blocks with log_warn/log_error.
+#
+# The in-memory buffer is exported as session_log.txt in the ZIP
+# download. For a full reference of logged events, see:
+# https://pharmaverse.github.io/aNCA/articles/session_log.html
+
+.log_env <- new.env(parent = emptyenv())
+.log_env$threshold <- "INFO"
+.log_env$buffer <- character(0)
+
+.LOG_LEVELS <- c(TRACE = 1L, DEBUG = 2L, INFO = 3L, SUCCESS = 4L, WARN = 5L, ERROR = 6L)
+
+#' Initialise the logging system.
+#'
+#' Reads the threshold from the `aNCA_LOG_LEVEL` environment variable
+#' (default `"INFO"`) and clears the in-memory log buffer.
+setup_logger <- function() {
+  level <- toupper(Sys.getenv("aNCA_LOG_LEVEL", "INFO"))
+  if (!level %in% names(.LOG_LEVELS)) level <- "INFO"
+  .log_env$threshold <- level
+  .log_env$buffer <- character(0)
+}
+
+#' Core logging function.
+#' @param level Character: one of the log level names.
+#' @param ... Message parts. If the first argument contains `{`, it is
+#'   evaluated as a glue string in the caller's environment. Otherwise
+#'   all arguments are pasted together.
+#' @noRd
+.log_msg <- function(level, ...) {
+  if (.LOG_LEVELS[[level]] < .LOG_LEVELS[[.log_env$threshold]]) return(invisible(NULL))
+
+  args <- list(...)
+  if (length(args) == 0L) {
+    msg <- ""
+  } else if (length(args) == 1L && grepl("\\{", args[[1]])) {
+    msg <- tryCatch(
+      glue::glue(args[[1]], .envir = parent.frame(2)),
+      error = function(e) paste0(args, collapse = "")
+    )
+  } else {
+    msg <- paste0(args, collapse = "")
+  }
+
+  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+  line <- paste0("[", timestamp, "] ", level, ": ", msg)
+
+  .log_env$buffer <- c(.log_env$buffer, line)
+  message(line)
+  invisible(NULL)
+}
+
+# Public log functions matching the logger API
+log_trace   <- function(...) .log_msg("TRACE", ...)
+log_debug   <- function(...) .log_msg("DEBUG", ...)
+log_info    <- function(...) .log_msg("INFO", ...)
+log_success <- function(...) .log_msg("SUCCESS", ...)
+log_warn    <- function(...) .log_msg("WARN", ...)
+log_error   <- function(...) .log_msg("ERROR", ...)
+
+#' Logs a list or data frame at DEBUG level.
+#'
+#' @param title Title for the log entry.
+#' @param l     List or data.frame to log.
+log_debug_list <- function(title, l) {
+  log_debug(aNCA:::.concatenate_list(title, l))
+}
+
+#' Return the in-memory log buffer as a character vector.
+#' @noRd
+get_log_buffer <- function() {
+  .log_env$buffer
+}
diff --git a/inst/shiny/functions/utils-exclusions.R b/inst/shiny/functions/utils-exclusions.R
index e16946cff..1372b358f 100644
--- a/inst/shiny/functions/utils-exclusions.R
+++ b/inst/shiny/functions/utils-exclusions.R
@@ -91,6 +91,12 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
     exclusion_list(append(current, list_new_reason))
     updateTextInput(session, "exclusion_reason", value = "")
     updateReactable(table_id, selected = NA)
+
+    type_label <- .exclusion_type_label(nca_checked, tlg_checked)
+    log_info(
+      "Exclusion added: ", length(rows_sel), " rows, type=", type_label,
+      ", reason='", reason, "'"
+    )
   }
 }
 
@@ -211,7 +217,8 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
 #' @param registered_ids reactiveVal holding character vector of registered IDs.
 #' @param input Shiny input object.
 #' @noRd
-.register_remove_observers <- function(exclusion_list, registered_ids, input) {
+.register_remove_observers <- function(exclusion_list, registered_ids, input,
+                                       on_remove = NULL) {
   lst <- exclusion_list()
   already <- registered_ids()
   new_ids <- setdiff(
@@ -223,6 +230,10 @@ EXCL_COLOR_PARAM <- "#FFF3CD"  # yellow — parameter exclusion
       local_id <- xbtn_id
       observeEvent(input[[local_id]], {
         current <- exclusion_list()
+        removed <- Filter(function(x) x$xbtn_id == local_id, current)
+        if (is.function(on_remove) && length(removed) > 0) {
+          on_remove(removed[[1]])
+        }
         exclusion_list(Filter(function(x) x$xbtn_id != local_id, current))
       }, ignoreInit = TRUE, once = TRUE)
     })
diff --git a/inst/shiny/functions/utils.R b/inst/shiny/functions/utils.R
index ae247ed42..ba264a160 100644
--- a/inst/shiny/functions/utils.R
+++ b/inst/shiny/functions/utils.R
@@ -1,45 +1,3 @@
-#' Sets up the logger package for the application.
-#'
-#' @details
-#' The application logs everything to a log file located in `/log` directory. If such folder
-#' does not exist, it will be created. Logfile for each session will be separate. The application
-#' will keep 5 log files at any given time - if this number is exceeded, the oldest log file
-#' will be deleted.
-#'
-#' In addition, information of the level specified by the user will be logged to console.
-#' As a default, this level is INFO - this is so that the user has good information on what is
-#' happening inside the app, but is not overwhelmed with tracing and debugging information. This
-#' level can be changed using `aNCA_LOG_LEVEL` environmental variable, set for example in
-#' `.Renviron` file.
-setup_logger <- function() {
-  log_layout(layout_glue_colors)
-  log_formatter(formatter_glue)
-  log_threshold(TRACE)
-  log_threshold(Sys.getenv("aNCA_LOG_LEVEL", "INFO"), index = 2)
-
-  log_dir <- "./log"
-  if (!dir.exists(log_dir)) dir.create(log_dir)
-  existing_logs <- list.files(log_dir, full.names = TRUE)
-  if (length(existing_logs) >= 5) file.remove(sort(existing_logs)[1]) # keep only five log files
-  logfile_name <- paste0(log_dir, "/aNCA_app_", format(Sys.time(), "%y%m%d-%H%M%S-"), ".log")
-
-  log_appender(appender_file(logfile_name))
-  log_appender(appender_console, index = 2)
-}
-
-#' Logs a list and data frame objects.
-#'
-#' @details
-#' Utilitary function for logging a list object (like mapping list or used settings) in
-#' a nice format. Parses a list into nice string and logs at DEBUG level. Can also process
-#' data frames, which will be converted into a list of rows.
-#'
-#' @param title Title for the logs.
-#' @param l     List object to be parsed into log. Can also be a data.frame.
-log_debug_list <- function(title, l) {
-  log_debug(aNCA:::.concatenate_list(title, l))
-}
-
 #' Needed to properly reset reactable.extras widgets
 #'
 #' @details
diff --git a/inst/shiny/functions/zip-utils.R b/inst/shiny/functions/zip-utils.R
index b4101c35e..1cdb1b23f 100644
--- a/inst/shiny/functions/zip-utils.R
+++ b/inst/shiny/functions/zip-utils.R
@@ -454,6 +454,12 @@ prepare_export_files <- function(target_dir,
                  detail = "Saving session info...")
     .export_session_info(target_dir)
   }
+
+  if ("session_log" %in% input$res_tree) {
+    progress$set(message = "Creating exports...",
+                 detail = "Saving session log...")
+    .export_session_log(target_dir)
+  }
   progress$inc(0.8)
 
   .clean_export_dir(target_dir, input, custom_names)
@@ -685,6 +691,45 @@ prepare_export_files <- function(target_dir,
   writeLines(lines, file.path(target_dir, "session_info.txt"))
 }
 
+#' Export the in-memory session log to a text file.
+#' @param target_dir Target directory for the export.
+#' @keywords internal
+.export_session_log <- function(target_dir) {
+  log_buffer <- get_log_buffer()
+
+  threshold <- .log_env$threshold
+  header <- c(
+    "# aNCA Session Log",
+    "#",
+    "# This file contains application events captured during your session.",
+    "# It records data upload, mapping, NCA settings, parameter selection,",
+    "# slope adjustments, exclusions, calculation results, and exports.",
+    "#",
+    "# Warnings and errors from these operations are included when caught",
+    "# by the application. Unexpected R errors or warnings from third-party",
+    "# packages that are not explicitly handled will NOT appear here.",
+    "#",
+    paste0("# Log level: ", threshold,
+           " (configurable via aNCA_LOG_LEVEL env var)"),
+    paste0("# Levels shown at current threshold: ",
+           paste(names(.LOG_LEVELS)[.LOG_LEVELS >= .LOG_LEVELS[[threshold]]],
+                 collapse = ", ")),
+    "#",
+    "# For a full reference of logged events, see:",
+    "# https://pharmaverse.github.io/aNCA/articles/session_log.html",
+    "#",
+    paste0("# Generated: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z")),
+    "# -------------------------------------------------------------------",
+    ""
+  )
+
+  if (length(log_buffer) == 0L) {
+    log_buffer <- "(No log entries captured during this session.)"
+  }
+
+  writeLines(c(header, log_buffer), file.path(target_dir, "session_log.txt"))
+}
+
 #' Clean Export Directory
 #' @param target_dir Target directory to clean
 #' @param input Shiny input object
@@ -722,6 +767,10 @@ prepare_export_files <- function(target_dir,
     files_req <- c(files_req, grep("session_info\\.txt$", all_files,
                                    value = TRUE))
   }
+  if ("session_log" %in% fnames) {
+    files_req <- c(files_req, grep("session_log\\.txt$", all_files,
+                                   value = TRUE))
+  }
   file.remove(all_files[!all_files %in% files_req])
 
   # Recursive directory cleanup — remove dirs that contain no files at any depth
diff --git a/inst/shiny/modules/tab_nca/setup/data_imputation.R b/inst/shiny/modules/tab_nca/setup/data_imputation.R
index eb5c5f6f9..a793c08ba 100644
--- a/inst/shiny/modules/tab_nca/setup/data_imputation.R
+++ b/inst/shiny/modules/tab_nca/setup/data_imputation.R
@@ -196,6 +196,15 @@ data_imputation_server <- function(id, settings_override) {
       }
     })
 
+    observeEvent(input$select_blq_strategy, {
+      log_info("BLQ imputation strategy changed: ", input$select_blq_strategy)
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$should_impute_c0, {
+      state <- if (isTRUE(input$should_impute_c0)) "enabled" else "disabled"
+      log_info("Start concentration imputation ", state)
+    }, ignoreInit = TRUE)
+
     blq_imputation_rule <- reactive({
       req(input$select_blq_strategy)
       rule_list <- switch(input$select_blq_strategy,
diff --git a/inst/shiny/modules/tab_nca/setup/general_exclusions.R b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
index 9a2fe9ce2..db118a3ed 100644
--- a/inst/shiny/modules/tab_nca/setup/general_exclusions.R
+++ b/inst/shiny/modules/tab_nca/setup/general_exclusions.R
@@ -131,6 +131,7 @@ general_exclusions_server <- function(
 
         xbtn_counter(max(new_ids))
         exclusion_list(rehydrated_list)
+        log_info("Exclusions restored from settings: ", length(overrides), " rules loaded")
       }
     })
 
@@ -166,7 +167,12 @@ general_exclusions_server <- function(
 
     # Register observers for new remove buttons (shared helper)
     observe({
-      .register_remove_observers(exclusion_list, registered_xbtns, input)
+      .register_remove_observers(
+        exclusion_list, registered_xbtns, input,
+        on_remove = function(item) {
+          log_info("Exclusion removed: reason='", item$reason, "'")
+        }
+      )
     })
 
     # Render the exclusions table (not shown if empty)
diff --git a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
index 163215844..967f1945d 100644
--- a/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
+++ b/inst/shiny/modules/tab_nca/setup/manual_slopes_table.R
@@ -84,7 +84,7 @@ manual_slopes_table_server <- function(
 
     # Add a new row to the table when the user clicks the add button
     observeEvent(input$add_rule, {
-      log_trace("{id}: adding manual slopes row")
+      log_trace("Slope selector: adding manual slope rule")
       first_group <- slopes_pknca_groups()[1, ]
       time_col <- pknca_data()$conc$columns$time
       new_row <- cbind(
@@ -121,7 +121,7 @@ manual_slopes_table_server <- function(
 
     # Remove selected rows from the table when the user clicks the remove button
     observeEvent(input$remove_rule, {
-      log_trace("{id}: removing manual slopes row")
+      log_trace("Slope selector: removing manual slope rule")
       req(manual_slopes())
       selected <- getReactableState("manual_slopes", "selected")
       req(selected)
@@ -135,7 +135,7 @@ manual_slopes_table_server <- function(
     # Render the manual slopes table (reactable)
     output$manual_slopes <- renderReactable({
       req(manual_slopes())
-      log_trace("{id}: rendering slope edit data table")
+      log_trace(id, ": rendering slope edit data table")
       isolate({
         data <- manual_slopes()
       })
diff --git a/inst/shiny/modules/tab_nca/setup/parameter_selection.R b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
index ea153562f..2cf04120d 100644
--- a/inst/shiny/modules/tab_nca/setup/parameter_selection.R
+++ b/inst/shiny/modules/tab_nca/setup/parameter_selection.R
@@ -318,6 +318,18 @@ parameter_selection_server <- function(id, processed_pknca_data, parameter_overr
       )
     })
 
+    # Log parameter selection changes (debounced to avoid noise from rapid clicks)
+    selections_debounced <- debounce(selections_state, 2000)
+    observeEvent(selections_debounced(), {
+      state <- selections_debounced()
+      req(state)
+      study_types <- study_types_list()
+      for (st in study_types) {
+        n_params <- sum(state[[st]], na.rm = TRUE)
+        log_info("Parameter selection for '", st, "': ", n_params, " parameters selected.")
+      }
+    }, ignoreInit = TRUE)
+
     observeEvent(input$clear_all, {
       state <- selections_state()
       req(state)
diff --git a/inst/shiny/modules/tab_nca/setup/settings.R b/inst/shiny/modules/tab_nca/setup/settings.R
index ceda5ae39..08958336d 100644
--- a/inst/shiny/modules/tab_nca/setup/settings.R
+++ b/inst/shiny/modules/tab_nca/setup/settings.R
@@ -252,6 +252,10 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     # A guard flag prevents infinite observer loops.
     updating_filters <- reactiveVal(FALSE)
 
+    # Guard to suppress log noise during initial data load / settings restore.
+    # Set to TRUE after the first analyte cascade completes.
+    filters_initialized <- reactiveVal(FALSE)
+
     # pending_settings holds the imported settings during the filter cascade.
     # The analyte observer reads it without clearing; the pcspec observer
     # consumes it (reads + clears). This ensures the override is available
@@ -287,7 +291,14 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       req(data(), input$select_analyte)
       if (updating_filters()) return()
       updating_filters(TRUE)
-      on.exit(updating_filters(FALSE))
+      on.exit({
+        updating_filters(FALSE)
+        if (!filters_initialized()) filters_initialized(TRUE)
+      })
+
+      if (filters_initialized()) {
+        log_info("Analyte selection changed: ", paste(input$select_analyte, collapse = ", "))
+      }
 
       settings <- pending_settings()
 
@@ -325,6 +336,10 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       updating_filters(TRUE)
       on.exit(updating_filters(FALSE))
 
+      if (filters_initialized()) {
+        log_info("Specimen selection changed: ", paste(input$select_pcspec, collapse = ", "))
+      }
+
       settings <- pending_settings()
       pending_settings(NULL)
 
@@ -347,6 +362,25 @@ settings_server <- function(id, data, adnca_data, settings_override) {
       .update_profile(settings)
     })
 
+    # Log profile, method, and min half-life points changes
+    observeEvent(input$select_profile, {
+      if (filters_initialized()) {
+        log_info("NCA profile changed: ", paste(input$select_profile, collapse = ", "))
+      }
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$method, {
+      if (filters_initialized()) {
+        log_info("Extrapolation method changed: ", input$method)
+      }
+    }, ignoreInit = TRUE)
+
+    observeEvent(input$min_hl_points, {
+      if (filters_initialized()) {
+        log_info("Min. half-life points changed: ", input$min_hl_points)
+      }
+    }, ignoreInit = TRUE)
+
     # Include keyboard limits for the settings GUI display
 
     # Keyboard limits for the setting thresholds
@@ -356,6 +390,19 @@ settings_server <- function(id, data, adnca_data, settings_override) {
     limit_input_value(input, session, "LAMZSPN_threshold", min = 0, lab = "LAMZSPN")
     limit_input_value(input, session, "min_hl_points", max = 10, min = 2, lab = "Min. HL Points")
 
+    # Log flag rule changes
+    lapply(c("R2ADJ", "R2", "AUCPEO", "AUCPEP", "LAMZSPN"), function(flag) {
+      rule_id <- paste0(flag, "_rule")
+      threshold_id <- paste0(flag, "_threshold")
+      observeEvent(input[[rule_id]], {
+        state <- if (input[[rule_id]]) "enabled" else "disabled"
+        log_info("Flag rule ", flag, " ", state)
+      }, ignoreInit = TRUE)
+      observeEvent(input[[threshold_id]], {
+        log_info("Flag rule ", flag, " threshold changed: ", input[[threshold_id]])
+      }, ignoreInit = TRUE)
+    })
+
     # Reactive value to store the partial intervals data table
     # Define the parameters that can be used for partial area calculations
     PARTIAL_INT_PARAMS <- metadata_nca_parameters %>%
diff --git a/inst/shiny/modules/tab_nca/setup/slope_selector.R b/inst/shiny/modules/tab_nca/setup/slope_selector.R
index 7f3cfe0f1..5c9f2a05c 100644
--- a/inst/shiny/modules/tab_nca/setup/slope_selector.R
+++ b/inst/shiny/modules/tab_nca/setup/slope_selector.R
@@ -246,6 +246,9 @@ slope_selector_server <- function( # nolint
     manual_slopes <- slopes_table$manual_slopes
     refresh_reactable <- slopes_table$refresh_reactable
 
+    # Track user-initiated slope changes (buttons, plotly clicks)
+    user_changed_slopes <- reactiveVal(FALSE)
+
     # Define the click events for the point exclusion and selection in the slope plots
     last_click_data <- reactiveVal(NULL)
     observeEvent(event_data("plotly_click", priority = "event"), {
@@ -259,6 +262,7 @@ slope_selector_server <- function( # nolint
       )
       # Update reactive values: last click & manual slopes table
       last_click_data(click_result$last_click_data)
+      user_changed_slopes(TRUE)
       manual_slopes(click_result$manual_slopes)
 
       # render rectable anew #
@@ -266,12 +270,25 @@ slope_selector_server <- function( # nolint
       refresh_reactable(refresh_reactable() + 1)
     })
 
+    # Also flag user-initiated changes from add/remove buttons
+    observeEvent(slopes_table$refresh_reactable(), {
+      user_changed_slopes(TRUE)
+    }, ignoreInit = TRUE)
+
     #' Separate event handling updating displayed reactable upon every change (adding and removing
     #' rows, plots selection, edits). This needs to be separate call, since simply re-rendering
     #' the table would mean losing focus on text inputs when entering values.
     observeEvent(manual_slopes(), {
       req(manual_slopes())
 
+      if (user_changed_slopes()) {
+        n_rules <- nrow(manual_slopes())
+        n_excl <- sum(manual_slopes()$TYPE == "Exclusion", na.rm = TRUE)
+        n_incl <- n_rules - n_excl
+        log_info("Slope rules updated: ", n_rules, " total (", n_incl, " selections, ", n_excl, " exclusions)")
+        user_changed_slopes(FALSE)
+      }
+
       # Update reactable with rules
       reactable::updateReactable(
         outputId = "manual_slopes",
diff --git a/inst/shiny/modules/tab_nca/zip.R b/inst/shiny/modules/tab_nca/zip.R
index 5334e49ac..2dd18d40e 100644
--- a/inst/shiny/modules/tab_nca/zip.R
+++ b/inst/shiny/modules/tab_nca/zip.R
@@ -759,7 +759,7 @@ zip_server <- function(id, res_nca, adnca_data, settings, grouping_vars) {
     }
     items$extras            <- TREE_LIST$extras
   } else {
-    items$extras <- TREE_LIST$extras[c("settings_file", "session_info")]
+    items$extras <- TREE_LIST$extras[c("settings_file", "session_info", "session_log")]
   }
 
   items
@@ -796,7 +796,8 @@ TREE_LIST <- list(
     results_slides = "",
     r_script = "",
     settings_file = "",
-    session_info = ""
+    session_info = "",
+    session_log = ""
   )
 )
 
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index c42ff1cdd..d980799f2 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -33,6 +33,8 @@ navbar:
           href: articles/adding_tlg.html
         - text: Design & Architecture
           href: articles/design.html
+        - text: Session Log Reference
+          href: articles/session_log.html
         - text: Functions manual
           href: reference/index.html
     project:
diff --git a/vignettes/session_log.Rmd b/vignettes/session_log.Rmd
new file mode 100644
index 000000000..7e0d08546
--- /dev/null
+++ b/vignettes/session_log.Rmd
@@ -0,0 +1,200 @@
+---
+title: "Session Log Reference"
+description: >
+  Reference for the session log exported with aNCA results.
+  Describes what events are captured, log levels, and configuration.
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Session Log Reference}
+  %\VignetteEngine{knitr::knitr}
+  %\VignetteEncoding{UTF-8}
+---
+
+When you export results as a ZIP file, aNCA includes a `session_log.txt` that
+records application events from your session. This page explains what the log
+contains, how to read it, and how to configure its verbosity.
+
+## What the log captures
+
+The session log records events emitted by explicit logging calls placed
+throughout the aNCA Shiny application. Each line follows this format:
+
+```
+[2025-04-30 09:40:16] INFO: Calculating NCA results...
+```
+
+The log captures **application-level events** — not raw R console output.
+Only messages that pass through aNCA's internal `log_*()` functions appear
+in the file.
+
+### What is NOT captured
+
+- Unexpected R warnings or errors that are not wrapped in a `tryCatch` block
+  with a corresponding `log_warn()` or `log_error()` call.
+- Messages from third-party packages (e.g., `PKNCA`, `dplyr`) unless the
+  application explicitly catches and logs them.
+- Raw `cat()` or `print()` output from any source.
+
+## Log levels
+
+aNCA uses six log levels, ordered from most to least verbose:
+
+| Level | Purpose |
+|---|---|
+| **TRACE** | Fine-grained internal operations (module attachment, reactive updates) |
+| **DEBUG** | Detailed diagnostic data (parameter lists, slope rule dumps) |
+| **INFO** | Key user-facing operations (data upload, NCA calculation, setting changes) |
+| **SUCCESS** | Completion confirmations (data loaded, results calculated) |
+| **WARN** | Non-fatal issues (calculation warnings, incompatible settings) |
+| **ERROR** | Failures (calculation errors, file load failures) |
+
+The default threshold is **INFO**, meaning only INFO, SUCCESS, WARN, and ERROR
+messages appear. Set `aNCA_LOG_LEVEL=TRACE` or `aNCA_LOG_LEVEL=DEBUG` in your
+`.Renviron` file to see more detail.
+
+## Logged events by workflow stage
+
+The following table lists all events currently captured in the session log,
+organized by the stage of the workflow where they occur.
+
+### Startup
+
+| Event | Level |
+|---|---|
+| Application startup | INFO |
+| Application restarting | INFO |
+
+### Data Upload
+
+| Event | Level |
+|---|---|
+| Data upload initialized (with file path) | INFO |
+| All user data loaded | SUCCESS |
+| File loading errors | ERROR |
+| User data binding errors | ERROR |
+
+### Settings Restore
+
+| Event | Level |
+|---|---|
+| Settings restored from version | SUCCESS |
+| Settings loaded from file | SUCCESS |
+| Settings load failure | ERROR |
+| Incompatible settings (analyte, profile, specimen) | WARN |
+
+### Data Mapping
+
+| Event | Level |
+|---|---|
+| Processing data mapping | INFO |
+| Data mapping warnings | WARN |
+| Data mapping errors | ERROR |
+
+### Data Filtering
+
+| Event | Level |
+|---|---|
+| Data filtering warnings | WARN |
+
+### NCA Settings
+
+| Event | Level |
+|---|---|
+| Analyte selection changed | INFO |
+| Specimen selection changed | INFO |
+| NCA profile selection changed | INFO |
+| Extrapolation method changed | INFO |
+| Min. half-life points changed | INFO |
+| Flag rule enabled/disabled | INFO |
+| Flag rule threshold changed | INFO |
+| BLQ imputation strategy changed | INFO |
+| Start concentration imputation toggled | INFO |
+
+### Parameter Selection
+
+| Event | Level |
+|---|---|
+| Parameter count per study type | INFO |
+
+### Slope Selector
+
+| Event | Level |
+|---|---|
+| Module server attachment | TRACE |
+| Plotly click detected | TRACE |
+| Manual slope rule added | INFO |
+| Manual slope rule removed | INFO |
+| Slope rules summary (inclusions/exclusions count) | DEBUG |
+| Manual slopes override applied | DEBUG |
+| Manual slopes override incompatible | WARN |
+| Slope edit table rendering | TRACE |
+
+### General Exclusions
+
+| Event | Level |
+|---|---|
+| Exclusion added (row count, type, reason) | INFO |
+| Exclusion removed | INFO |
+| Exclusions restored from settings | INFO |
+
+### NCA Calculation
+
+| Event | Level |
+|---|---|
+| Creating / updating PKNCA data object | TRACE |
+| PKNCA data object created | SUCCESS |
+| PKNCA data object creation error | ERROR |
+| Updating parameter selection data | TRACE |
+| Calculating NCA results | INFO |
+| NCA calculation warnings | WARN |
+| NCA results calculated | SUCCESS |
+| NCA calculation error | ERROR |
+| Invalid parameters | ERROR |
+
+### Exploration Plots
+
+| Event | Level |
+|---|---|
+| Rendering individual plots | INFO |
+| Computing mean plot | INFO |
+| Rendering boxplot | INFO |
+| Exploration plot saved (with overwrite flag) | INFO |
+| Exploration plot removed | INFO |
+
+### TLG Generation
+
+| Event | Level |
+|---|---|
+| TLG module server attachment | TRACE |
+| Submitted TLG list | DEBUG |
+| TLG list rendering error | ERROR |
+
+### Export
+
+| Event | Level |
+|---|---|
+| Downloading summary statistics as CSV | INFO |
+
+### Units & Other
+
+| Event | Level |
+|---|---|
+| Applying custom units specification | TRACE |
+
+## Configuring the log level
+
+Set the `aNCA_LOG_LEVEL` environment variable before starting the app.
+Valid values: `TRACE`, `DEBUG`, `INFO` (default), `SUCCESS`, `WARN`, `ERROR`.
+
+In your `.Renviron` file:
+
+```
+aNCA_LOG_LEVEL=DEBUG
+```
+
+Or set it in R before launching:
+
+```r
+Sys.setenv(aNCA_LOG_LEVEL = "TRACE")
+aNCA::run_app()
+```