diff --git a/src/cargo/util/config/mod.rs b/src/cargo/util/config/mod.rs
index 0e161ba8af4..901357dbc59 100644
--- a/src/cargo/util/config/mod.rs
+++ b/src/cargo/util/config/mod.rs
@@ -1507,7 +1507,7 @@ impl Config {
         let possible_with_extension = dir.join(format!("{}.toml", filename_without_extension));
 
         if possible.exists() {
-            if warn && possible_with_extension.exists() {
+            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
@@ -1520,12 +1520,22 @@ impl Config {
                 };
 
                 if !skip_warning {
-                    self.shell().warn(format!(
-                        "Both `{}` and `{}` exist. Using `{}`",
-                        possible.display(),
-                        possible_with_extension.display(),
-                        possible.display()
-                    ))?;
+                    if possible_with_extension.exists() {
+                        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`"),
+                        )?;
+                    }
                 }
             }
 
diff --git a/tests/testsuite/config.rs b/tests/testsuite/config.rs
index e02cd445d90..39bc30e41e0 100644
--- a/tests/testsuite/config.rs
+++ b/tests/testsuite/config.rs
@@ -275,7 +275,10 @@ f1 = 1
 
     // It should NOT have warned for the symlink.
     let output = read_output(config);
-    assert_match("", &output);
+    let expected = "\
+warning: `[ROOT]/.cargo/config` is deprecated in favor of `config.toml`
+note: If you need to support cargo 1.38 or earlier, you can symlink `config` to `config.toml`";
+    assert_match(expected, &output);
 }
 
 #[cargo_test]