diff --git a/Cargo.toml b/Cargo.toml
index d0f2afb3972..38d0f5bb4e0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -184,6 +184,7 @@ rand.workspace = true
 regex.workspace = true
 rusqlite.workspace = true
 rustfix.workspace = true
+same-file.workspace = true
 semver.workspace = true
 serde = { workspace = true, features = ["derive"] }
 serde-untagged.workspace = true
diff --git a/src/cargo/util/context/mod.rs b/src/cargo/util/context/mod.rs
index 507e6a6ad14..914d57f2138 100644
--- a/src/cargo/util/context/mod.rs
+++ b/src/cargo/util/context/mod.rs
@@ -1537,36 +1537,32 @@ impl GlobalContext {
         let possible = dir.join(filename_without_extension);
         let possible_with_extension = dir.join(format!("{}.toml", filename_without_extension));
 
-        if possible.exists() {
+        if let Ok(possible_handle) = same_file::Handle::from_path(&possible) {
             if warn {
-                // We don't want to print a warning if the version
-                // without the extension is just a symlink to the version
-                // WITH an extension, which people may want to do to
-                // support multiple Cargo versions at once and not
-                // get a warning.
-                let skip_warning = if let Ok(target_path) = fs::read_link(&possible) {
-                    target_path == possible_with_extension
-                } else {
-                    false
-                };
-
-                if !skip_warning {
-                    if possible_with_extension.exists() {
+                if let Ok(possible_with_extension_handle) =
+                    same_file::Handle::from_path(&possible_with_extension)
+                {
+                    // We don't want to print a warning if the version
+                    // without the extension is just a symlink to the version
+                    // WITH an extension, which people may want to do to
+                    // support multiple Cargo versions at once and not
+                    // get a warning.
+                    if possible_handle != possible_with_extension_handle {
                         self.shell().warn(format!(
                             "both `{}` and `{}` exist. Using `{}`",
                             possible.display(),
                             possible_with_extension.display(),
                             possible.display()
                         ))?;
-                    } else {
-                        self.shell().warn(format!(
-                            "`{}` is deprecated in favor of `{filename_without_extension}.toml`",
-                            possible.display(),
-                        ))?;
-                        self.shell().note(
-                            format!("if you need to support cargo 1.38 or earlier, you can symlink `{filename_without_extension}` to `{filename_without_extension}.toml`"),
-                        )?;
                     }
+                } else {
+                    self.shell().warn(format!(
+                        "`{}` is deprecated in favor of `{filename_without_extension}.toml`",
+                        possible.display(),
+                    ))?;
+                    self.shell().note(
+                        format!("if you need to support cargo 1.38 or earlier, you can symlink `{filename_without_extension}` to `{filename_without_extension}.toml`"),
+                    )?;
                 }
             }
 
diff --git a/tests/testsuite/config.rs b/tests/testsuite/config.rs
index 39fcee2cd73..2ad81486dc9 100644
--- a/tests/testsuite/config.rs
+++ b/tests/testsuite/config.rs
@@ -184,12 +184,29 @@ fn symlink_file(target: &Path, link: &Path) -> io::Result<()> {
     os::windows::fs::symlink_file(target, link)
 }
 
-fn symlink_config_to_config_toml() {
+fn make_config_symlink_to_config_toml_absolute() {
     let toml_path = paths::root().join(".cargo/config.toml");
     let symlink_path = paths::root().join(".cargo/config");
     t!(symlink_file(&toml_path, &symlink_path));
 }
 
+fn make_config_symlink_to_config_toml_relative() {
+    let symlink_path = paths::root().join(".cargo/config");
+    t!(symlink_file(Path::new("config.toml"), &symlink_path));
+}
+
+fn rename_config_toml_to_config_replacing_with_symlink() {
+    let root = paths::root();
+    t!(fs::rename(
+        root.join(".cargo/config.toml"),
+        root.join(".cargo/config")
+    ));
+    t!(symlink_file(
+        Path::new("config"),
+        &root.join(".cargo/config.toml")
+    ));
+}
+
 #[track_caller]
 pub fn assert_error<E: Borrow<anyhow::Error>>(error: E, msgs: &str) {
     let causes = error
@@ -298,7 +315,33 @@ f1 = 1
 ",
     );
 
-    symlink_config_to_config_toml();
+    make_config_symlink_to_config_toml_absolute();
+
+    let gctx = new_gctx();
+
+    assert_eq!(gctx.get::<Option<i32>>("foo.f1").unwrap(), Some(1));
+
+    // It should NOT have warned for the symlink.
+    let output = read_output(gctx);
+    assert_match("", &output);
+}
+
+#[cargo_test]
+fn config_ambiguous_filename_symlink_doesnt_warn_relative() {
+    // Windows requires special permissions to create symlinks.
+    // If we don't have permission, just skip this test.
+    if !symlink_supported() {
+        return;
+    };
+
+    write_config_toml(
+        "\
+[foo]
+f1 = 1
+",
+    );
+
+    make_config_symlink_to_config_toml_relative();
 
     let gctx = new_gctx();
 
@@ -309,6 +352,32 @@ f1 = 1
     assert_match("", &output);
 }
 
+#[cargo_test]
+fn config_ambiguous_filename_symlink_doesnt_warn_backward() {
+    // Windows requires special permissions to create symlinks.
+    // If we don't have permission, just skip this test.
+    if !symlink_supported() {
+        return;
+    };
+
+    write_config_toml(
+        "\
+[foo]
+f1 = 1
+",
+    );
+
+    rename_config_toml_to_config_replacing_with_symlink();
+
+    let gctx = new_gctx();
+
+    assert_eq!(gctx.get::<Option<i32>>("foo.f1").unwrap(), Some(1));
+
+    // It should NOT have warned for this situation.
+    let output = read_output(gctx);
+    assert_match("", &output);
+}
+
 #[cargo_test]
 fn config_ambiguous_filename() {
     write_config_extless(