diff --git a/sklearn/cluster/_hdbscan/meson.build b/sklearn/cluster/_hdbscan/meson.build
index f2e3ac91b1eb2..8d880b39a4db5 100644
--- a/sklearn/cluster/_hdbscan/meson.build
+++ b/sklearn/cluster/_hdbscan/meson.build
@@ -1,7 +1,7 @@
 cluster_hdbscan_extension_metadata = {
   '_linkage': {'sources': [cython_gen.process('_linkage.pyx'), metrics_cython_tree]},
   '_reachability': {'sources': [cython_gen.process('_reachability.pyx')]},
-  '_tree': {'sources': ['_tree.pyx']}
+  '_tree': {'sources': [cython_gen.process('_tree.pyx')]}
 }
 
 foreach ext_name, ext_dict : cluster_hdbscan_extension_metadata
diff --git a/sklearn/meson.build b/sklearn/meson.build
index 93de0c18d99f9..30feb944029d3 100644
--- a/sklearn/meson.build
+++ b/sklearn/meson.build
@@ -219,7 +219,7 @@ extensions = ['_isotonic']
 
 py.extension_module(
   '_isotonic',
-  '_isotonic.pyx',
+  cython_gen.process('_isotonic.pyx'),
   cython_args: cython_args,
   install: true,
   subdir: 'sklearn',
diff --git a/sklearn/neighbors/meson.build b/sklearn/neighbors/meson.build
index df2aab466500c..7993421896218 100644
--- a/sklearn/neighbors/meson.build
+++ b/sklearn/neighbors/meson.build
@@ -39,7 +39,7 @@ neighbors_extension_metadata = {
   '_partition_nodes':
       {'sources': [cython_gen_cpp.process('_partition_nodes.pyx')],
        'dependencies': [np_dep]},
-  '_quad_tree': {'sources': ['_quad_tree.pyx'], 'dependencies': [np_dep]},
+  '_quad_tree': {'sources': [cython_gen.process('_quad_tree.pyx')], 'dependencies': [np_dep]},
 }
 
 foreach ext_name, ext_dict : neighbors_extension_metadata
diff --git a/sklearn/utils/meson.build b/sklearn/utils/meson.build
index 9ac2454172c9a..ae490e987a4ff 100644
--- a/sklearn/utils/meson.build
+++ b/sklearn/utils/meson.build
@@ -20,7 +20,7 @@ utils_extension_metadata = {
   '_cython_blas': {'sources': [cython_gen.process('_cython_blas.pyx')]},
   'arrayfuncs': {'sources': [cython_gen.process('arrayfuncs.pyx')]},
   'murmurhash': {
-      'sources': ['murmurhash.pyx', 'src' / 'MurmurHash3.cpp'],
+      'sources': [cython_gen.process('murmurhash.pyx'), 'src' / 'MurmurHash3.cpp'],
   },
   '_fast_dict':
     {'sources': [cython_gen_cpp.process('_fast_dict.pyx')]},