diff --git a/docs/doxygen/Doxyfile b/docs/doxygen/Doxyfile
index c7d11a8369..15ec9ea487 100644
--- a/docs/doxygen/Doxyfile
+++ b/docs/doxygen/Doxyfile
@@ -802,8 +802,8 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = build \
-                         "../JUCE Module Format.md" \
-                         "../CMake API.md"
+                         "build/JUCE Module Format.md" \
+                         "build/CMake API.md"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/docs/doxygen/process_source_files.py b/docs/doxygen/process_source_files.py
index d9862ff708..c38135dabe 100644
--- a/docs/doxygen/process_source_files.py
+++ b/docs/doxygen/process_source_files.py
@@ -173,3 +173,8 @@ if __name__ == "__main__":
     # Create an extra header file containing the module hierarchy.
     with open(os.path.join(args.dest_dir, "juce_modules.dox"), "w") as f:
         f.write("\r\n\r\n".join(module_definitions))
+
+    # Copy markdown docs
+    for name in ["JUCE Module Format.md", "CMake API.md"]:
+        shutil.copyfile(os.path.join(args.source_dir, "..", "docs", name),
+                        os.path.join(args.dest_dir, name))