diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index 44e522868..2064e2f81 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -1601,7 +1601,7 @@ class NinjaBackend(backends.Backend):
                     # TODO: introspection?
                     cython_sources.append(output)
                 else:
-                    generated_sources[ssrc] = mesonlib.File.from_built_file(gen.subdir, ssrc)
+                    generated_sources[ssrc] = mesonlib.File.from_built_file(gen.get_subdir(), ssrc)
 
         return static_sources, generated_sources, cython_sources
 
diff --git a/test cases/cython/2 generated sources/meson.build b/test cases/cython/2 generated sources/meson.build
index 89dacfa55..cfe62602d 100644
--- a/test cases/cython/2 generated sources/meson.build	
+++ b/test cases/cython/2 generated sources/meson.build	
@@ -26,6 +26,16 @@ test(
   env : ['PYTHONPATH=' + meson.current_build_dir()]
 )
 
+# Test a CustomTargetIndex
+cti = custom_target(
+  'cti',
+  input : 'gen.py',
+  output : 'cti.pyx',
+  command : [py3, '@INPUT@', '@OUTPUT@'],
+)
+
+cti_ext = py3.extension_module('cti', cti[0], dependencies : py3_dep)
+
 cf = configure_file(
   input : 'configure.pyx.in',
   output : 'cf.pyx',