diff --git a/CLAUDE.md b/CLAUDE.md
index f180de7..1a42edb 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -156,6 +156,19 @@ docs/damocles-migration.md   options for moving damocles onto hyperhive
   marks them `failed` with note `"agent state dir missing"` so they fall out
   of `pending`. They stay in sqlite for audit.
 
+## Auto-update on startup
+
+`hive-c0re serve` runs `auto_update::run` in a background task right after
+opening the coordinator. It enumerates sub-agent containers (manager
+excluded — its config comes from the host's NixOS module) and rebuilds any
+whose recorded hyperhive rev differs from the current one. Rev = canonical
+filesystem path of `cfg.hyperhiveFlake` (so `/etc/hyperhive` resolving to a
+new `/nix/store/...-source` triggers a rebuild). Marker file:
+`/var/lib/hyperhive/applied/.<name>.hyperhive-rev`. If the flake input has
+no canonical path (e.g. a `github:` URL), auto-update is a no-op — rebuild
+manually. The task is async and never blocks the admin socket; failures are
+logged and don't take the daemon down.
+
 ## Build / deploy / test
 
 ```sh
diff --git a/hive-c0re/src/auto_update.rs b/hive-c0re/src/auto_update.rs
new file mode 100644
index 0000000..609e064
--- /dev/null
+++ b/hive-c0re/src/auto_update.rs
@@ -0,0 +1,118 @@
+//! Startup auto-update: on `hive-c0re serve` boot, rebuild any sub-agent
+//! container whose recorded "hyperhive rev" differs from the current one,
+//! then write the new rev as the marker. Skips rebuild when nothing changed
+//! so warm restarts are near-free.
+//!
+//! "Rev" is the canonical filesystem path of the configured hyperhive flake
+//! (e.g. `/nix/store/<hash>-source` when `/etc/hyperhive` is a symlink the
+//! NixOS module wires up). For non-path flake URLs we don't have a cheap rev
+//! signal, so auto-update is a no-op — operators rebuild manually.
+
+use std::path::{Path, PathBuf};
+use std::sync::Arc;
+
+use anyhow::Result;
+
+use crate::coordinator::Coordinator;
+use crate::lifecycle::{self, AGENT_PREFIX};
+
+/// Marker file recording the hyperhive rev a sub-agent's container was last
+/// built against. Sibling of `applied/<name>/` (rather than inside it) to
+/// keep it out of the applied repo's git history.
+fn rev_marker_path(name: &str) -> PathBuf {
+    PathBuf::from(format!("/var/lib/hyperhive/applied/.{name}.hyperhive-rev"))
+}
+
+/// Resolve the current rev of `hyperhive_flake`. For a path on disk we
+/// canonicalize (following symlinks) so a /etc/hyperhive → /nix/store/...
+/// update yields a different string. For anything else we return None.
+fn current_flake_rev(hyperhive_flake: &str) -> Option<String> {
+    let path = Path::new(hyperhive_flake);
+    if !path.exists() {
+        return None;
+    }
+    std::fs::canonicalize(path)
+        .ok()
+        .map(|p| p.display().to_string())
+}
+
+/// Rebuild every sub-agent whose marker differs from the current rev. Logs
+/// per-agent outcomes and continues past failures. Returns Ok even if some
+/// rebuilds failed — startup shouldn't be blocked by a broken agent.
+pub async fn run(coord: Arc<Coordinator>) -> Result<()> {
+    let Some(current_rev) = current_flake_rev(&coord.hyperhive_flake) else {
+        tracing::info!(
+            flake = %coord.hyperhive_flake,
+            "auto-update: hyperhive_flake has no canonical path; skipping",
+        );
+        return Ok(());
+    };
+    tracing::info!(rev = %current_rev, "auto-update: scanning agents");
+
+    let containers = match lifecycle::list().await {
+        Ok(c) => c,
+        Err(e) => {
+            tracing::warn!(error = ?e, "auto-update: nixos-container list failed");
+            return Ok(());
+        }
+    };
+
+    let mut tasks = Vec::new();
+    for container in containers {
+        let Some(name) = container.strip_prefix(AGENT_PREFIX) else {
+            continue;
+        };
+        let name = name.to_owned();
+        let marker = rev_marker_path(&name);
+        let prev = std::fs::read_to_string(&marker).ok();
+        if prev.as_deref().map(str::trim) == Some(current_rev.as_str()) {
+            tracing::debug!(%name, "auto-update: up-to-date");
+            continue;
+        }
+
+        let coord = coord.clone();
+        let current_rev = current_rev.clone();
+        tasks.push(tokio::spawn(async move {
+            tracing::info!(
+                %name,
+                prev = ?prev,
+                rev = %current_rev,
+                "auto-update: rebuilding agent",
+            );
+            let agent_dir = match coord.register_agent(&name) {
+                Ok(d) => d,
+                Err(e) => {
+                    tracing::warn!(%name, error = ?e, "auto-update: register_agent failed");
+                    return;
+                }
+            };
+            let applied_dir = Coordinator::agent_applied_dir(&name);
+            let claude_dir = Coordinator::agent_claude_dir(&name);
+            match lifecycle::rebuild(
+                &name,
+                &coord.hyperhive_flake,
+                &agent_dir,
+                &applied_dir,
+                &claude_dir,
+            )
+            .await
+            {
+                Ok(()) => {
+                    if let Err(e) = std::fs::write(&marker, &current_rev) {
+                        tracing::warn!(%name, error = ?e, "auto-update: write rev marker failed");
+                    } else {
+                        tracing::info!(%name, "auto-update: agent rebuilt");
+                    }
+                }
+                Err(e) => {
+                    tracing::warn!(%name, error = ?e, "auto-update: rebuild failed");
+                }
+            }
+        }));
+    }
+
+    for t in tasks {
+        let _ = t.await;
+    }
+    Ok(())
+}
diff --git a/hive-c0re/src/main.rs b/hive-c0re/src/main.rs
index 1db132d..d47f424 100644
--- a/hive-c0re/src/main.rs
+++ b/hive-c0re/src/main.rs
@@ -8,6 +8,7 @@ use hive_sh4re::{HostRequest, HostResponse};
 mod actions;
 mod agent_server;
 mod approvals;
+mod auto_update;
 mod broker;
 mod client;
 mod coordinator;
@@ -85,6 +86,15 @@ async fn main() -> Result<()> {
             dashboard_port,
         } => {
             let coord = Arc::new(Coordinator::open(&db, hyperhive_flake)?);
+            // Run auto-update in the background — don't block service start.
+            // Operators sometimes need the admin socket up to debug a stuck
+            // agent, and the rebuild loop can take tens of seconds.
+            let update_coord = coord.clone();
+            tokio::spawn(async move {
+                if let Err(e) = auto_update::run(update_coord).await {
+                    tracing::warn!(error = ?e, "auto-update task failed");
+                }
+            });
             manager_server::start(coord.clone())?;
             let dash_coord = coord.clone();
             tokio::spawn(async move {