diff --git a/lib/crates/fabro-cli/src/install.rs b/lib/crates/fabro-cli/src/install.rs
index 8181a0bdf..3183cae1f 100644
--- a/lib/crates/fabro-cli/src/install.rs
+++ b/lib/crates/fabro-cli/src/install.rs
@@ -914,7 +914,7 @@ pub async fn run_install() -> Result<()> {
     eprintln!();
     eprintln!(
         "  Setup complete! Go to your project and run {} to get started.",
-        s.bold_cyan.apply_to("fabro init")
+        s.bold_cyan.apply_to("fabro repo init")
     );
     Ok(())
 }
diff --git a/lib/crates/fabro-cli/src/main.rs b/lib/crates/fabro-cli/src/main.rs
index bf7b96a66..76b89b0ac 100644
--- a/lib/crates/fabro-cli/src/main.rs
+++ b/lib/crates/fabro-cli/src/main.rs
@@ -114,7 +114,8 @@ enum Command {
         #[arg(long)]
         dry_run: bool,
     },
-    /// Initialize a new project
+    /// Initialize a new project (deprecated: use `repo init`)
+    #[command(hide = true)]
     Init,
     /// Set up the Fabro environment (LLMs, certs, GitHub)
     Install,
@@ -148,6 +149,11 @@ enum Command {
     Docs,
     /// Upgrade fabro to the latest version
     Upgrade(upgrade::UpgradeArgs),
+    /// Repository commands
+    Repo {
+        #[command(subcommand)]
+        command: RepoCommand,
+    },
     /// System maintenance commands
     System {
         #[command(subcommand)]
@@ -189,6 +195,12 @@ enum SystemCommand {
     Df(commands::runs::DfArgs),
 }
 
+#[derive(Subcommand)]
+enum RepoCommand {
+    /// Initialize a new project
+    Init,
+}
+
 #[derive(Subcommand)]
 enum SkillCommand {
     /// Install a built-in skill
@@ -436,6 +448,9 @@ async fn main_inner() -> (String, Result<()>) {
         #[cfg(feature = "server")]
         Command::Serve(_) => "serve",
         Command::Doctor { .. } => "doctor",
+        Command::Repo { command } => match command {
+            RepoCommand::Init => "repo init",
+        },
         Command::Init => "init",
         Command::Install => "install",
         Command::Ps(_) => "ps",
@@ -506,7 +521,11 @@ async fn main_inner() -> (String, Result<()>) {
 
     let upgrade_handle = if matches!(
         cli.command,
-        Command::Run(_) | Command::Exec(_) | Command::Init | Command::Install
+        Command::Run(_)
+            | Command::Exec(_)
+            | Command::Repo { .. }
+            | Command::Init
+            | Command::Install
     ) {
         upgrade::spawn_upgrade_check(cli.no_upgrade_check, upgrade_check_enabled)
     } else {
@@ -760,7 +779,16 @@ async fn main_inner() -> (String, Result<()>) {
             Command::Docs => {
                 open::that("https://docs.fabro.sh/")?;
             }
+            Command::Repo { command } => match command {
+                RepoCommand::Init => {
+                    init::run_init().await?;
+                }
+            },
             Command::Init => {
+                eprintln!(
+                    "{} `fabro init` is deprecated, use `fabro repo init` instead",
+                    console::Style::new().yellow().apply_to("warning:")
+                );
                 init::run_init().await?;
             }
             Command::Install => {
diff --git a/lib/crates/fabro-cli/tests/cmd/repo/help.trycmd b/lib/crates/fabro-cli/tests/cmd/repo/help.trycmd
new file mode 100644
index 000000000..5fe17b3da
--- /dev/null
+++ b/lib/crates/fabro-cli/tests/cmd/repo/help.trycmd
@@ -0,0 +1,6 @@
+```console
+$ fabro repo --help
+[..]
+...
+
+```
diff --git a/lib/crates/fabro-cli/tests/trycmd.rs b/lib/crates/fabro-cli/tests/trycmd.rs
index dca631493..f4a432055 100644
--- a/lib/crates/fabro-cli/tests/trycmd.rs
+++ b/lib/crates/fabro-cli/tests/trycmd.rs
@@ -17,6 +17,7 @@ trycmd_subcommand!(cli_install, "install");
 trycmd_subcommand!(cli_llm, "llm");
 trycmd_subcommand!(cli_model, "model");
 trycmd_subcommand!(cli_pr, "pr");
+trycmd_subcommand!(cli_repo, "repo");
 trycmd_subcommand!(cli_preview, "preview");
 trycmd_subcommand!(cli_run, "run");
 trycmd_subcommand!(cli_ssh, "ssh");