diff --git a/mesonbuild/backend/ninjabackend.py b/mesonbuild/backend/ninjabackend.py
index 2e6e351c9..e00dd5eea 100644
--- a/mesonbuild/backend/ninjabackend.py
+++ b/mesonbuild/backend/ninjabackend.py
@@ -1131,9 +1131,14 @@ int dummy;
             # file is outside the build directory, the path components will be
             # stripped and just the basename will be used.
             if isinstance(gensrc, (build.CustomTarget, build.GeneratedList)) or gensrc.is_built:
-                vala_c_file = os.path.splitext(vala_file)[0] + '.c'
-            else:
                 vala_c_file = os.path.splitext(os.path.basename(vala_file))[0] + '.c'
+            else:
+                realpath = os.path.abspath(os.path.join(self.environment.get_build_dir(), vala_file))
+                if (realpath.startswith(os.path.join(self.environment.get_source_dir(), target.get_subdir()))):
+                    relpath = os.path.relpath(realpath, os.path.join(self.environment.get_source_dir(), target.get_subdir()))
+                    vala_c_file = os.path.join(os.path.dirname(relpath), os.path.splitext(os.path.basename(vala_file))[0] + '.c')
+                else:
+                    vala_c_file = os.path.splitext(os.path.basename(vala_file))[0] + '.c'
             # All this will be placed inside the c_out_dir
             vala_c_file = os.path.join(c_out_dir, vala_c_file)
             vala_c_src.append(vala_c_file)
@@ -1145,6 +1150,7 @@ int dummy;
         # means it will also preserve the directory components of Vala sources
         # found inside the build tree (generated sources).
         args += ['-d', c_out_dir]
+        args += ['-b', os.path.join(self.environment.get_source_dir(), target.get_subdir())]
         if not isinstance(target, build.Executable):
             # Library name
             args += ['--library=' + target.name]
diff --git a/test cases/vala/22 same target in directories/Subdir/Test.vala b/test cases/vala/22 same target in directories/Subdir/Test.vala
new file mode 100644
index 000000000..3a311f4dc
--- /dev/null
+++ b/test cases/vala/22 same target in directories/Subdir/Test.vala	
@@ -0,0 +1,5 @@
+public class Subdir.Test : GLib.Object {
+    construct {
+        stdout.printf("Test from subdir.\n");
+    }
+}
diff --git a/test cases/vala/22 same target in directories/Test.vala b/test cases/vala/22 same target in directories/Test.vala
new file mode 100644
index 000000000..1b57dd96d
--- /dev/null
+++ b/test cases/vala/22 same target in directories/Test.vala	
@@ -0,0 +1,5 @@
+public class Test : GLib.Object {
+    construct {
+        stdout.printf("Test from main directory.\n");
+    }
+}
diff --git a/test cases/vala/22 same target in directories/meson.build b/test cases/vala/22 same target in directories/meson.build
new file mode 100644
index 000000000..25250da1a
--- /dev/null
+++ b/test cases/vala/22 same target in directories/meson.build	
@@ -0,0 +1,11 @@
+project('valatest', 'vala', 'c')
+
+valadeps = [dependency('glib-2.0'), dependency('gobject-2.0')]
+valafiles = files([
+    'prog.vala',
+    'Test.vala',
+    'Subdir/Test.vala'
+])
+
+e = executable('multidir_prog', valafiles, dependencies : valadeps)
+test('valatest', e)
diff --git a/test cases/vala/22 same target in directories/prog.vala b/test cases/vala/22 same target in directories/prog.vala
new file mode 100644
index 000000000..f3ac09977
--- /dev/null
+++ b/test cases/vala/22 same target in directories/prog.vala	
@@ -0,0 +1,9 @@
+class MainProg : GLib.Object {
+
+    public static int main(string[] args) {
+        var test1 = new Test ();
+        var test2 = new Subdir.Test ();
+        stdout.printf("Vala is working.\n");
+        return 0;
+    }
+}