diff --git a/mesonbuild/backend/backends.py b/mesonbuild/backend/backends.py
index ea4f255c8..2dbf1ec57 100644
--- a/mesonbuild/backend/backends.py
+++ b/mesonbuild/backend/backends.py
@@ -408,6 +408,9 @@ class Backend:
             # common cases.
             exe_cmd = [self.get_target_filename_abs(exe)]
             exe_for_machine = MachineChoice.BUILD
+        elif isinstance(exe, mesonlib.File):
+            exe_cmd = [exe.rel_to_builddir(self.environment.source_dir)]
+            exe_for_machine = MachineChoice.BUILD
         else:
             exe_cmd = [exe]
             exe_for_machine = MachineChoice.BUILD
diff --git a/test cases/common/52 run target/meson.build b/test cases/common/52 run target/meson.build
index 49e8d75b0..d1964e89f 100644
--- a/test cases/common/52 run target/meson.build	
+++ b/test cases/common/52 run target/meson.build	
@@ -65,11 +65,14 @@ conf = configure_file(
   configuration: configuration_data()
 )
 
-
 run_target('configure_script',
   command : conf
 )
 
+custom_target('configure_script_ct',
+  command: conf,
+  output: 'dummy.txt',
+  capture: true)
 
 # Target names that clash with potential builtin functionality.
 run_target('ctags',