diff --git a/src/cargo/util/context/mod.rs b/src/cargo/util/context/mod.rs
index 1db5b9a3c987..ec75cc02e77c 100644
--- a/src/cargo/util/context/mod.rs
+++ b/src/cargo/util/context/mod.rs
@@ -1577,25 +1577,27 @@ impl GlobalContext {
         }
     }
 
-    fn walk_tree<F>(&self, pwd: &Path, home: &Path, mut walk: F) -> CargoResult<()>
+    fn walk_tree<F>(&self, pwd: &Path, cargo_home: &Path, mut walk: F) -> CargoResult<()>
     where
         F: FnMut(&Path) -> CargoResult<()>,
     {
         let mut stash: HashSet<PathBuf> = HashSet::new();
 
         for current in paths::ancestors(pwd, self.search_stop_path.as_deref()) {
+            // Be aware `current` may be the parent of the `$CARGO_HOME`, in this case the next line also walk the `$CARGO_HOME`.
             if let Some(path) = self.get_file_path(&current.join(".cargo"), "config", true)? {
                 walk(&path)?;
                 stash.insert(path);
             }
         }
 
-        // Once we're done, also be sure to walk the home directory even if it's not
-        // in our history to be sure we pick up that standard location for
-        // information.
-        if let Some(path) = self.get_file_path(home, "config", true)? {
-            if !stash.contains(&path) {
-                walk(&path)?;
+        let cargo_home_parent = cargo_home.parent().unwrap_or(cargo_home);
+        // If we haven't walked the $CARGO_HOME directory yet, walk it to pick up that standard location for information.
+        if !pwd.starts_with(cargo_home_parent) {
+            if let Some(path) = self.get_file_path(cargo_home, "config", true)? {
+                if !stash.contains(&path) {
+                    walk(&path)?;
+                }
             }
         }
 
diff --git a/tests/testsuite/config.rs b/tests/testsuite/config.rs
index aba4e2552b58..1c6eff4477f7 100644
--- a/tests/testsuite/config.rs
+++ b/tests/testsuite/config.rs
@@ -315,8 +315,6 @@ f1 = 1
         .with_stderr_data(str![[r#"
 [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`
-[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`
 
 "#]])
         .run();