diff --git a/CMakeLists.txt b/CMakeLists.txt
index 920d15835e9..9fe77d5536a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -576,6 +576,16 @@ endif()
 
 set(rel_cachedir var/trafficserver)
 
+if(EXISTS "${PROJECT_SOURCE_DIR}/include/ink_autoconf.h")
+  message(STATUS "Autoconf build detected in source tree. Removing autoconf headers.")
+endif()
+
+# In-tree autoconf configuration causes duplicate definitions of some symbols
+# in generated headers. If the files don't exist, no error is emitted.
+file(REMOVE "${PROJECT_SOURCE_DIR}/include/tscore/ink_config.h")
+file(REMOVE "${PROJECT_SOURCE_DIR}/include/ts/apidefs.h")
+file(REMOVE "${PROJECT_SOURCE_DIR}/include/ink_autoconf.h")
+
 configure_file(configs/storage.config.default.in configs/storage.config.default)
 configure_file(configs/records.yaml.default.in configs/records.yaml.default)
 configure_file(include/tscore/ink_config.h.cmake.in include/tscore/ink_config.h)