diff --git a/build_scripts/build_versioned_docs.py b/build_scripts/build_versioned_docs.py
index 4bdc87d9..ff457b43 100644
--- a/build_scripts/build_versioned_docs.py
+++ b/build_scripts/build_versioned_docs.py
@@ -65,14 +65,15 @@ def build_docs(worktree: Path, output_dir: Path, release_name: str | None) -> No
     output_dir.mkdir(parents=True, exist_ok=True)
     env = os.environ.copy()
 
-    run(["doxygen", "Doxyfile"], cwd=docs_dir, env=env)
+    src_dir = worktree / "src"
+    run(["doxygen", "docs/Doxyfile"], cwd=src_dir, env=env)
 
     sphinx_command = [
         "sphinx-build",
         "-b",
         "html",
         "-D",
-        "breathe_projects.rawtoaces=doxygen/xml",
+        "breathe_projects.rawtoaces=../doxygen/xml",
     ]
 
     if release_name is not None:
diff --git a/src/docs/Doxyfile b/src/docs/Doxyfile
index e67706a8..240fa03d 100644
--- a/src/docs/Doxyfile
+++ b/src/docs/Doxyfile
@@ -8,7 +8,7 @@ PROJECT_BRIEF          = "RAW to ACES Utility"
 PROJECT_LOGO           =
 
 # Input/Output
-INPUT                  = ../../include/rawtoaces
+INPUT                  = ../include/rawtoaces
 OUTPUT_DIRECTORY       = doxygen
 RECURSIVE              = YES
 FILE_PATTERNS          = *.h *.hpp