diff --git a/src/cargo/ops/fix.rs b/src/cargo/ops/fix.rs
index a5b94919240..6e4c718fcd4 100644
--- a/src/cargo/ops/fix.rs
+++ b/src/cargo/ops/fix.rs
@@ -61,6 +61,7 @@ use crate::ops::resolve::WorkspaceResolve;
 use crate::ops::{self, CompileOptions};
 use crate::util::diagnostic_server::{Message, RustfixDiagnosticServer};
 use crate::util::errors::CargoResult;
+use crate::util::toml_mut::manifest::LocalManifest;
 use crate::util::GlobalContext;
 use crate::util::{existing_vcs_repo, LockServer, LockServerClient};
 use crate::{drop_eprint, drop_eprintln};
@@ -272,7 +273,8 @@ fn migrate_manifests(ws: &Workspace<'_>, pkgs: &[&Package]) -> CargoResult<()> {
             MaybePackage::Virtual(manifest) => manifest.original_toml(),
         };
         if Edition::Edition2024 <= prepare_for_edition {
-            let mut document = pkg.manifest().document().clone().into_mut();
+            let mut manifest_mut = LocalManifest::try_new(pkg.manifest_path())?;
+            let document = &mut manifest_mut.data;
             let mut fixes = 0;
 
             let root = document.as_table_mut();
@@ -335,9 +337,7 @@ fn migrate_manifests(ws: &Workspace<'_>, pkgs: &[&Package]) -> CargoResult<()> {
                 let msg = format!("{file} ({fixes} {verb})");
                 ws.gctx().shell().status("Fixed", msg)?;
 
-                let s = document.to_string();
-                let new_contents_bytes = s.as_bytes();
-                cargo_util::paths::write_atomic(pkg.manifest_path(), new_contents_bytes)?;
+                manifest_mut.write()?;
             }
         }
     }
diff --git a/tests/testsuite/edition.rs b/tests/testsuite/edition.rs
index 7b22c2dbda8..2c6ea53b08b 100644
--- a/tests/testsuite/edition.rs
+++ b/tests/testsuite/edition.rs
@@ -135,7 +135,7 @@ fn unset_edition_with_unset_rust_version() {
 
     p.cargo("check -v")
         .with_stderr_data(str![[r#"
-[WARNING] no edition set: defaulting to the 2015 edition while the latest is 2024
+[WARNING] no edition set: defaulting to the 2015 edition while the latest is [..]
 [CHECKING] foo v0.1.0 ([ROOT]/foo)
 [RUNNING] `rustc [..] --edition=2015 [..]`
 [FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
diff --git a/tests/testsuite/fix.rs b/tests/testsuite/fix.rs
index bd47056c0dc..685f664803e 100644
--- a/tests/testsuite/fix.rs
+++ b/tests/testsuite/fix.rs
@@ -2446,6 +2446,65 @@ edition = "2021"
     );
 }
 
+#[cargo_test]
+fn migrate_removes_project_for_script() {
+    let p = project()
+        .file(
+            "foo.rs",
+            r#"
+---
+# Before package
+[ package ] # After package header
+# After package header line
+name = "foo"
+edition = "2021"
+# After package table
+
+# Before project
+[ project ] # After project header
+# After project header line
+name = "foo"
+edition = "2021"
+# After project table
+---
+
+fn main() {
+}
+"#,
+        )
+        .build();
+
+    p.cargo("-Zscript fix --edition --allow-no-vcs --manifest-path foo.rs")
+        .masquerade_as_nightly_cargo(&["script"])
+        .with_stderr_data(str![[r#"
+[MIGRATING] foo.rs from 2021 edition to 2024
+[FIXED] foo.rs (1 fix)
+[CHECKING] foo v0.0.0 ([ROOT]/foo)
+[MIGRATING] [ROOT]/home/.cargo/target/[HASH]/foo.rs from 2021 edition to 2024
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+    assert_e2e().eq(
+        p.read_file("foo.rs"),
+        str![[r#"
+
+---
+# Before package
+[ package ] # After package header
+# After package header line
+name = "foo"
+edition = "2021"
+# After project table
+---
+
+fn main() {
+}
+
+"#]],
+    );
+}
+
 #[cargo_test]
 fn migrate_rename_underscore_fields() {
     let p = project()
diff --git a/tests/testsuite/publish.rs b/tests/testsuite/publish.rs
index 961af6ad088..51ab6cfdaf7 100644
--- a/tests/testsuite/publish.rs
+++ b/tests/testsuite/publish.rs
@@ -142,6 +142,7 @@ fn duplicate_version() {
                 [package]
                 name = "foo"
                 version = "0.0.1"
+                edition = "2015"
                 authors = []
                 license = "MIT"
                 description = "foo"
@@ -160,7 +161,6 @@ See https://doc.rust-lang.org/cargo/reference/manifest.html#package-metadata for
 [PACKAGING] foo v0.0.1 ([ROOT]/foo)
 [PACKAGED] 4 files, [FILE_SIZE]B ([FILE_SIZE]B compressed)
 [VERIFYING] foo v0.0.1 ([ROOT]/foo)
-[WARNING] no edition set: defaulting to the 2015 edition while the latest is 2024
 [COMPILING] foo v0.0.1 ([ROOT]/foo/target/package/foo-0.0.1)
 [FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
 [UPLOADING] foo v0.0.1 ([ROOT]/foo)