diff --git a/desktop/src-tauri/src/lib.rs b/desktop/src-tauri/src/lib.rs
index f419a761b..f63a79f46 100644
--- a/desktop/src-tauri/src/lib.rs
+++ b/desktop/src-tauri/src/lib.rs
@@ -499,6 +499,7 @@ pub fn run() {
             // restore_managed_agents_on_launch (which reads managed-agents.json).
             migration::sync_shared_agent_data(&app_handle);
             migration::reconcile_persona_pack_paths(&app_handle);
+            migration::reconcile_provider_mcp_commands(&app_handle);
             migration::migrate_persona_provider_to_runtime(&app_handle);
 
             // Resolve persisted identity key (env var → file → generate+save).
diff --git a/desktop/src-tauri/src/managed_agents/runtime.rs b/desktop/src-tauri/src/managed_agents/runtime.rs
index e7ba8277a..cca31c72c 100644
--- a/desktop/src-tauri/src/managed_agents/runtime.rs
+++ b/desktop/src-tauri/src/managed_agents/runtime.rs
@@ -797,14 +797,20 @@ pub fn spawn_agent_child(
     let agent_args = normalize_agent_args(&record.agent_command, record.agent_args.clone());
     let resolved_acp_command = resolve_command(&record.acp_command)
         .ok_or_else(|| missing_command_message(&record.acp_command, "ACP harness command"))?;
-    let resolved_mcp_command: Option<std::path::PathBuf> =
-        if record.mcp_command.is_empty() {
-            None
-        } else {
-            Some(resolve_command(&record.mcp_command).ok_or_else(|| {
-                missing_command_message(&record.mcp_command, "MCP server command")
-            })?)
-        };
+    let resolved_mcp_command: Option<std::path::PathBuf> = if record.mcp_command.is_empty() {
+        None
+    } else {
+        match resolve_command(&record.mcp_command) {
+            Some(path) => Some(path),
+            None => {
+                eprintln!(
+                    "sprout-desktop: mcp_command {:?} not found, skipping",
+                    record.mcp_command
+                );
+                None
+            }
+        }
+    };
     // Resolve agent command to a full path (DMG launches have minimal PATH).
     let resolved_agent_command = resolve_command(&record.agent_command)
         .map(|p| p.display().to_string())
diff --git a/desktop/src-tauri/src/migration.rs b/desktop/src-tauri/src/migration.rs
index 8b1436eb2..eda5cae74 100644
--- a/desktop/src-tauri/src/migration.rs
+++ b/desktop/src-tauri/src/migration.rs
@@ -318,6 +318,65 @@ pub fn reconcile_persona_pack_paths(app: &tauri::AppHandle) {
     reconcile_pack_paths_in_file(&path, &canonical_dir);
 }
 
+fn reconcile_mcp_commands_in_file(path: &Path) {
+    patch_json_records(path, |obj| {
+        let agent_command = match obj.get("agent_command").and_then(|v| v.as_str()) {
+            Some(cmd) => cmd.to_string(),
+            None => return false,
+        };
+        let Some(runtime) = crate::managed_agents::known_acp_runtime(&agent_command) else {
+            return false;
+        };
+        let expected = runtime.mcp_command.unwrap_or("");
+        let current = obj
+            .get("mcp_command")
+            .and_then(|v| v.as_str())
+            .unwrap_or("");
+        if current == expected {
+            return false;
+        }
+        // Only fix values that are clearly stale (empty or a removed binary).
+        // Leave user-customized values untouched.
+        if !current.is_empty() && current != "sprout-mcp-server" {
+            return false;
+        }
+        eprintln!(
+            "sprout-desktop: runtime-reconcile: {:?} ({:?}): mcp_command {:?} → {:?}",
+            obj.get("name").and_then(|v| v.as_str()).unwrap_or("?"),
+            agent_command,
+            current,
+            expected,
+        );
+        obj.insert(
+            "mcp_command".to_string(),
+            serde_json::Value::String(expected.to_string()),
+        );
+        true
+    });
+}
+
+/// Reconcile `mcp_command` values in managed-agents.json against the
+/// discovery table. Known runtimes get their canonical mcp_command;
+/// unknown/custom agents are left untouched. Covers both the current
+/// app data dir and the canonical dev data dir (for worktree instances).
+pub fn reconcile_provider_mcp_commands(app: &tauri::AppHandle) {
+    let Ok(current_dir) = app.path().app_data_dir() else {
+        return;
+    };
+    let mut dirs = vec![current_dir.clone()];
+    if let Some(canonical) = canonical_dev_data_dir(&current_dir) {
+        if canonical.exists() && canonical != current_dir {
+            dirs.push(canonical);
+        }
+    }
+    for dir in dirs {
+        let path = dir.join("agents/managed-agents.json");
+        if path.exists() {
+            reconcile_mcp_commands_in_file(&path);
+        }
+    }
+}
+
 fn rename_provider_to_runtime_in_personas(path: &Path) {
     patch_json_records(path, |obj| {
         if obj.contains_key("runtime") {
@@ -899,4 +958,118 @@ mod tests {
         // provider key should still be there since the closure returns false when runtime exists
         assert_eq!(records[0]["provider"], "old-value");
     }
+
+    #[test]
+    fn reconcile_mcp_commands_clears_stale_sprout_mcp_server() {
+        let dir = tempfile::tempdir().unwrap();
+        write_agents_json(
+            dir.path(),
+            &serde_json::json!([{
+                "name": "Solo",
+                "agent_command": "goose",
+                "mcp_command": "sprout-mcp-server"
+            }]),
+        );
+        reconcile_mcp_commands_in_file(&dir.path().join("agents/managed-agents.json"));
+        let records = read_agents_json(dir.path());
+        assert_eq!(records[0]["mcp_command"], "");
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_sets_canonical_for_sprout_agent() {
+        let dir = tempfile::tempdir().unwrap();
+        write_agents_json(
+            dir.path(),
+            &serde_json::json!([{
+                "name": "Stilgar",
+                "agent_command": "sprout-agent",
+                "mcp_command": "sprout-mcp-server"
+            }]),
+        );
+        reconcile_mcp_commands_in_file(&dir.path().join("agents/managed-agents.json"));
+        let records = read_agents_json(dir.path());
+        assert_eq!(records[0]["mcp_command"], "sprout-dev-mcp");
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_leaves_custom_value_untouched() {
+        let dir = tempfile::tempdir().unwrap();
+        let json = serde_json::json!([{
+            "name": "Solo",
+            "agent_command": "goose",
+            "mcp_command": "my-custom-mcp"
+        }]);
+        write_agents_json(dir.path(), &json);
+        let path = dir.path().join("agents/managed-agents.json");
+        let before = std::fs::read_to_string(&path).unwrap();
+        reconcile_mcp_commands_in_file(&path);
+        assert_eq!(before, std::fs::read_to_string(&path).unwrap());
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_leaves_unknown_runtime_untouched() {
+        let dir = tempfile::tempdir().unwrap();
+        let json = serde_json::json!([{
+            "name": "Custom",
+            "agent_command": "my-custom-agent",
+            "mcp_command": "sprout-mcp-server"
+        }]);
+        write_agents_json(dir.path(), &json);
+        let path = dir.path().join("agents/managed-agents.json");
+        let before = std::fs::read_to_string(&path).unwrap();
+        reconcile_mcp_commands_in_file(&path);
+        assert_eq!(before, std::fs::read_to_string(&path).unwrap());
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_is_idempotent() {
+        let dir = tempfile::tempdir().unwrap();
+        write_agents_json(
+            dir.path(),
+            &serde_json::json!([{
+                "name": "Solo",
+                "agent_command": "goose",
+                "mcp_command": "sprout-mcp-server"
+            }]),
+        );
+        let path = dir.path().join("agents/managed-agents.json");
+        reconcile_mcp_commands_in_file(&path);
+        let after_first = std::fs::read_to_string(&path).unwrap();
+        reconcile_mcp_commands_in_file(&path);
+        assert_eq!(after_first, std::fs::read_to_string(&path).unwrap());
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_handles_mixed_agents() {
+        let dir = tempfile::tempdir().unwrap();
+        write_agents_json(
+            dir.path(),
+            &serde_json::json!([
+                {"name": "Stale Goose", "agent_command": "goose", "mcp_command": "sprout-mcp-server"},
+                {"name": "Clean Goose", "agent_command": "goose", "mcp_command": ""},
+                {"name": "Custom Agent", "agent_command": "goose", "mcp_command": "my-custom-mcp"},
+                {"name": "Stale Sprout", "agent_command": "sprout-agent", "mcp_command": "sprout-mcp-server"}
+            ]),
+        );
+        reconcile_mcp_commands_in_file(&dir.path().join("agents/managed-agents.json"));
+        let records = read_agents_json(dir.path());
+        assert_eq!(records[0]["mcp_command"], "");
+        assert_eq!(records[1]["mcp_command"], "");
+        assert_eq!(records[2]["mcp_command"], "my-custom-mcp");
+        assert_eq!(records[3]["mcp_command"], "sprout-dev-mcp");
+    }
+
+    #[test]
+    fn reconcile_mcp_commands_skips_record_without_agent_command() {
+        let dir = tempfile::tempdir().unwrap();
+        let json = serde_json::json!([{
+            "name": "No Command",
+            "mcp_command": "sprout-mcp-server"
+        }]);
+        write_agents_json(dir.path(), &json);
+        let path = dir.path().join("agents/managed-agents.json");
+        let before = std::fs::read_to_string(&path).unwrap();
+        reconcile_mcp_commands_in_file(&path);
+        assert_eq!(before, std::fs::read_to_string(&path).unwrap());
+    }
 }