diff --git a/crates/uv/src/commands/tool/update_shell.rs b/crates/uv/src/commands/tool/update_shell.rs
index 36cf7c91cdcd..f306d80fea23 100644
--- a/crates/uv/src/commands/tool/update_shell.rs
+++ b/crates/uv/src/commands/tool/update_shell.rs
@@ -73,7 +73,12 @@ pub(crate) async fn update_shell(printer: Printer) -> Result<ExitStatus> {
         // Search for the command in the file, to avoid redundant updates.
         match fs_err::tokio::read_to_string(&file).await {
             Ok(contents) => {
-                if contents.contains(&command) {
+                if contents
+                    .lines()
+                    .map(str::trim)
+                    .filter(|line| !line.starts_with('#'))
+                    .any(|line| line.contains(&command))
+                {
                     debug!(
                         "Skipping already-updated configuration file: {}",
                         file.simplified_display()