diff --git a/CHANGELOG.md b/CHANGELOG.md
index 261bd15..412faa3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,9 @@ Instead, changes appear below grouped by the date they were added to the workflo
 
 ## 2025
 
+* 26 September 2025: Updated workflow compatibility declaration in `nextstrain-pathogen.yaml`.
+  **This requires Nextstrain CLI >=10.3.0** to setup and update the pathogen without error messages.
+  However, workflows will still run with Nextstrain CLI <10.3.0 [#69][]
 * 24 September 2025: Implemented augur subsample, replacing augur filter steps for both genome and N450 workflows. **This is a breaking change**. [#70][]
     - Replaces `augur filter` calls with `augur subsample`.
     - Replaces `filter` and `filter_N450` with `subsample` section in the config.yaml.
@@ -27,6 +30,7 @@ Instead, changes appear below grouped by the date they were added to the workflo
 [#61]: https://github.com/nextstrain/measles/pull/61
 [#62]: https://github.com/nextstrain/measles/pull/62
 [#68]: https://github.com/nextstrain/measles/pull/68
+[#69]: https://github.com/nextstrain/measles/pull/69
 [#70]: https://github.com/nextstrain/measles/pull/70
 [nextstrain/shared]: https://github.com/nextstrain/shared
 
diff --git a/nextstrain-pathogen.yaml b/nextstrain-pathogen.yaml
index 9a723f0..16abff0 100644
--- a/nextstrain-pathogen.yaml
+++ b/nextstrain-pathogen.yaml
@@ -6,5 +6,13 @@
 # This file's *contents* is the "registration metadata" for the pathogen repo,
 # used by `nextstrain setup` and `nextstrain run`.
 ---
-compatibility:
-  nextstrain run: true
+workflows:
+  ingest:
+    compatibility:
+      nextstrain run: True
+  phylogenetic:
+    compatibility:
+      nextstrain run: True
+  nextclade:
+    compatibility:
+      nextstrain run: True