diff --git a/cmake/TargetCapnpSources.cmake b/cmake/TargetCapnpSources.cmake
index 2334e260..172986f4 100644
--- a/cmake/TargetCapnpSources.cmake
+++ b/cmake/TargetCapnpSources.cmake
@@ -121,5 +121,13 @@ function(target_capnp_sources target include_prefix)
   # dependencies of generated headers on other generated headers.
   if(NOT TARGET "${target}_headers")
     add_custom_target("${target}_headers" DEPENDS ${generated_headers})
+  else()
+    # target_capnp_sources can be called more than once for the same target,
+    # for example to add optional schemas or schemas with a different include
+    # prefix. Dependencies can't be added to an existing custom target, so add
+    # these headers through a helper target that ${target}_headers depends on.
+    string(MD5 headers_hash "${CMAKE_CURRENT_SOURCE_DIR};${generated_headers}")
+    add_custom_target("${target}_headers_${headers_hash}" DEPENDS ${generated_headers})
+    add_dependencies("${target}_headers" "${target}_headers_${headers_hash}")
   endif()
 endfunction()