diff --git a/R/use_extendr.R b/R/use_extendr.R
index 00336bfd..b28fb9df 100644
--- a/R/use_extendr.R
+++ b/R/use_extendr.R
@@ -121,14 +121,14 @@ use_extendr <- function(
 
   use_rextendr_template(
     "cleanup",
-    save_as = file.path("src", "cleanup"),
+    save_as = file.path("cleanup"),
     quiet = quiet,
     overwrite = overwrite
   )
 
   use_rextendr_template(
     "cleanup.win",
-    save_as = file.path("src", "cleanup.win"),
+    save_as = file.path("cleanup.win"),
     quiet = quiet,
     overwrite = overwrite
   )
diff --git a/inst/templates/settings.json b/inst/templates/settings.json
index 9b0fd0dc..da4ad80d 100644
--- a/inst/templates/settings.json
+++ b/inst/templates/settings.json
@@ -3,8 +3,10 @@
     "${workspaceFolder}/src/rust/Cargo.toml"
   ],
   "files.associations": {
+    "Makevars": "makefile",
     "Makevars.in": "makefile",
     "Makevars.win": "makefile",
+    "Makevars.win.in": "makefile",
     "configure": "shellscript",
     "configure.win": "shellscript",
     "cleanup": "shellscript",
diff --git a/tests/testthat/_snaps/use_extendr.md b/tests/testthat/_snaps/use_extendr.md
index 96c19051..ce1a9b8d 100644
--- a/tests/testthat/_snaps/use_extendr.md
+++ b/tests/testthat/_snaps/use_extendr.md
@@ -375,8 +375,8 @@
       > File 'src/entrypoint.c' already exists. Skip writing the file.
       > File 'src/Makevars.in' already exists. Skip writing the file.
       > File 'src/Makevars.win.in' already exists. Skip writing the file.
-      > File 'src/cleanup' already exists. Skip writing the file.
-      > File 'src/cleanup.win' already exists. Skip writing the file.
+      > File 'cleanup' already exists. Skip writing the file.
+      > File 'cleanup.win' already exists. Skip writing the file.
       > File 'src/.gitignore' already exists. Skip writing the file.
       > File 'src/rust/Cargo.toml' already exists. Skip writing the file.
       > File 'src/rust/src/lib.rs' already exists. Skip writing the file.
@@ -398,8 +398,8 @@
       v Writing 'src/entrypoint.c'
       v Writing 'src/Makevars.in'
       v Writing 'src/Makevars.win.in'
-      v Writing 'src/cleanup'
-      v Writing 'src/cleanup.win'
+      v Writing 'cleanup'
+      v Writing 'cleanup.win'
       v Writing 'src/.gitignore'
       v Writing 'src/rust/Cargo.toml'
       v Writing 'src/rust/src/lib.rs'