diff --git a/doc/internal-api/doxygen.cfg.in b/doc/internal-api/doxygen.cfg.in
index 73fba6948..662fb4333 100644
--- a/doc/internal-api/doxygen.cfg.in
+++ b/doc/internal-api/doxygen.cfg.in
@@ -33,32 +33,7 @@ GENERATE_LATEX         = NO
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-# FIXME Make this list more maintainable somehow. We could maybe generate this
-# in the Makefile, but we would need to change how `.in` files are preprocessed
-# so they can expand variables despite configure variables.
-
-INPUT                  = \
-  src/libcmd \
-  src/libexpr \
-  src/libexpr/flake \
-  tests/unit/libexpr \
-  tests/unit/libexpr/value \
-  tests/unit/libexpr/test \
-  tests/unit/libexpr/test/value \
-  src/libexpr/value \
-  src/libfetchers \
-  src/libmain \
-  src/libstore \
-  src/libstore/build \
-  src/libstore/builtins \
-  tests/unit/libstore \
-  tests/unit/libstore/test \
-  src/libutil \
-  tests/unit/libutil \
-  tests/unit/libutil/test \
-  src/nix \
-  src/nix-env \
-  src/nix-store
+INPUT                  = @INPUT_PATHS@
 
 # If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
 # in the source code. If set to NO, only conditional compilation will be
@@ -97,3 +72,15 @@ EXPAND_AS_DEFINED      = \
   DECLARE_WORKER_SERIALISER \
   DECLARE_SERVE_SERIALISER \
   LENGTH_PREFIXED_PROTO_HELPER
+
+# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
+# Stripping is only done if one of the specified strings matches the left-hand
+# part of the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the path to
+# strip.
+#
+# Note that you can specify absolute paths here, but also relative paths, which
+# will be relative from the directory where doxygen is started.
+# This tag requires that the tag FULL_PATH_NAMES is set to YES.
+
+STRIP_FROM_PATH        = "@PROJECT_SOURCE_ROOT@"
diff --git a/doc/internal-api/meson.build b/doc/internal-api/meson.build
index faa30f194..af93b6943 100644
--- a/doc/internal-api/meson.build
+++ b/doc/internal-api/meson.build
@@ -1,3 +1,35 @@
+internal_api_sources = [
+  'src/libcmd',
+  'src/libexpr',
+  'src/libexpr/flake',
+  'tests/unit/libexpr',
+  'tests/unit/libexpr/value',
+  'tests/unit/libexpr/test',
+  'tests/unit/libexpr/test/value',
+  'src/libexpr/value',
+  'src/libfetchers',
+  'src/libmain',
+  'src/libstore',
+  'src/libstore/build',
+  'src/libstore/builtins',
+  'tests/unit/libstore',
+  'tests/unit/libstore/test',
+  'src/libutil',
+  'tests/unit/libutil',
+  'tests/unit/libutil/test',
+  'src/nix',
+  'src/nix-env',
+  'src/nix-store',
+]
+
+# We feed Doxygen absolute paths so it can be invoked from any working directory.
+internal_api_sources_absolute = []
+foreach src : internal_api_sources
+  internal_api_sources_absolute += '"' + (meson.project_source_root() / src) + '"'
+endforeach
+
+internal_api_sources_oneline = ' \\\n  '.join(internal_api_sources_absolute)
+
 doxygen_cfg = configure_file(
   input : 'doxygen.cfg.in',
   output : 'doxygen.cfg',
@@ -5,22 +37,16 @@ doxygen_cfg = configure_file(
     'PACKAGE_VERSION': meson.project_version(),
     'RAPIDCHECK_HEADERS': rapidcheck_meson.get_variable('includedir'),
     'docdir' : meson.current_build_dir(),
+    'INPUT_PATHS' : internal_api_sources_oneline,
+    'PROJECT_SOURCE_ROOT' : meson.project_source_root(),
   },
 )
 
 internal_api_docs = custom_target(
   'internal-api-docs',
   command : [
-    bash,
-    # Meson can you please just give us a `workdir` argument to custom targets...
-    '-c',
-    # We have to prefix the doxygen_cfg path with the project build root
-    # because of the cd in front.
-    'cd @0@ && @1@ @2@/@INPUT0@'.format(
-      meson.project_source_root(),
-      doxygen.full_path(),
-      meson.project_build_root(),
-    ),
+    doxygen.full_path(),
+    '@INPUT0@',
   ],
   input : [
     doxygen_cfg,