diff --git a/cmake/cfe-common.doxyfile.in b/cmake/cfe-common.doxyfile.in
index 9a8720a4b..bea09e0e3 100644
--- a/cmake/cfe-common.doxyfile.in
+++ b/cmake/cfe-common.doxyfile.in
@@ -54,7 +54,6 @@ GENERATE_DEPRECATEDLIST= YES
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
 WARN_NO_PARAMDOC       = YES
-WARN_LOGFILE           = @CMAKE_BINARY_DIR@/doc/warnings.log
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
diff --git a/cmake/cfe-usersguide.doxyfile.in b/cmake/cfe-usersguide.doxyfile.in
index 3b2166d36..969303aa0 100644
--- a/cmake/cfe-usersguide.doxyfile.in
+++ b/cmake/cfe-usersguide.doxyfile.in
@@ -9,6 +9,7 @@ INPUT                 += @MISSION_SOURCE_DIR@/cfe/docs/src/main.dox
 @INCLUDE               = @MISSION_BINARY_DIR@/doc/cfe-common.doxyfile
 PROJECT_NAME           = "Core Flight Executive Users Guide"
 OUTPUT_DIRECTORY       = @CMAKE_BINARY_DIR@/doc/users_guide
+WARN_LOGFILE           = @CMAKE_BINARY_DIR@/doc/cfe-usersguide-warnings.log
 GENERATE_LATEX         = YES
 
 # For purposes of the user guide, reference the "stock" mission configuration
diff --git a/cmake/mission-detaildesign.doxyfile.in b/cmake/mission-detaildesign.doxyfile.in
index 180f87522..fe7c1f9d8 100644
--- a/cmake/mission-detaildesign.doxyfile.in
+++ b/cmake/mission-detaildesign.doxyfile.in
@@ -7,6 +7,7 @@
 PROJECT_NAME           = "@MISSION_NAME@"
 PROJECT_BRIEF          = "Core Flight System project built using \"@MISSIONCONFIG@\" configuration"
 OUTPUT_DIRECTORY       = @CMAKE_BINARY_DIR@/doc/detaildesign
+WARN_LOGFILE           = @CMAKE_BINARY_DIR@/doc/detaildesign-warnings.log
 
 INPUT                 += @MISSION_DEFS@
 STRIP_FROM_PATH       += @MISSION_DEFS@