diff --git a/justfile b/justfile
index b7d02a5c3..a89778f40 100644
--- a/justfile
+++ b/justfile
@@ -277,6 +277,10 @@ dev *ARGS: _ensure-sidecar-stubs
     cd {{desktop_dir}}
     [[ -d node_modules ]] || pnpm install
     source ../scripts/instance-env.sh
+    # Ctrl+C kills the Tauri app before its in-process sweep finishes, leaking
+    # agent workers. Reap this instance's agents on exit as a backstop.
+    INSTANCE_ID=$(node -e "console.log(JSON.parse(process.env.SPROUT_TAURI_CONFIG).identifier)")
+    trap '../scripts/cleanup-instance-agents.sh "$INSTANCE_ID"' EXIT
     echo "Starting on Vite port ${SPROUT_VITE_PORT}, relay ${SPROUT_RELAY_URL}"
     pnpm exec tauri dev --features mesh-llm --config "$SPROUT_TAURI_CONFIG" {{ARGS}}
 
@@ -294,6 +298,10 @@ staging *ARGS: _ensure-sidecar-stubs
     cd {{desktop_dir}}
     source ../scripts/instance-env.sh
     export SPROUT_RELAY_URL="wss://sprout-oss.stage.blox.sqprod.co"
+    # Ctrl+C kills the Tauri app before its in-process sweep finishes, leaking
+    # agent workers. Reap this instance's agents on exit as a backstop.
+    INSTANCE_ID=$(node -e "console.log(JSON.parse(process.env.SPROUT_TAURI_CONFIG).identifier)")
+    trap '../scripts/cleanup-instance-agents.sh "$INSTANCE_ID"' EXIT
     echo "Starting staging on Vite port ${SPROUT_VITE_PORT}, relay ${SPROUT_RELAY_URL}"
     pnpm exec tauri dev --features mesh-llm --config "$SPROUT_TAURI_CONFIG" {{ARGS}}
 
diff --git a/scripts/cleanup-instance-agents.sh b/scripts/cleanup-instance-agents.sh
new file mode 100755
index 000000000..a6bc52f98
--- /dev/null
+++ b/scripts/cleanup-instance-agents.sh
@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+# Reap the agent processes belonging to a single desktop instance.
+#
+# `tauri dev` Ctrl+C tears down the Rust app before its in-process system sweep
+# can finish, so agent workers (goose, sprout-agent, ...) it spawned in their
+# own process groups survive as orphans. This script is the shell-side backstop:
+# run it from an EXIT trap in the `just dev`/`just staging` recipes.
+#
+# It reads the PID-file receipts the desktop already writes — one file per agent
+# under `<app-data>/agents/agent-pids/<pubkey>.pid`, each containing the agent's
+# PGID (agents are spawned with `process_group(0)`, so PID == PGID). Killing by
+# PGID reaches the whole agent subtree. We deliberately do NOT match the
+# `SPROUT_MANAGED_AGENT` env var from the shell: on macOS `pkill -f` matches only
+# argv, not the environment, so an env-marker match silently reaps nothing.
+#
+# Scoping is exact because the app-data directory is keyed by the instance's
+# bundle identifier, so this only ever touches the receipts this instance wrote
+# (the main checkout never reaps a worktree's agents, or vice versa).
+#
+# Usage: cleanup-instance-agents.sh <instance-id>
+#   <instance-id> is the desktop bundle identifier, e.g. `xyz.block.sprout.app.dev`
+#   (main checkout) or `xyz.block.sprout.app.dev.my-branch` (a worktree).
+
+set -euo pipefail
+
+instance_id="${1:-}"
+if [[ -z "$instance_id" ]]; then
+    echo "cleanup-instance-agents: no instance id given, skipping" >&2
+    exit 0
+fi
+
+case "$(uname -s)" in
+    Darwin) app_data="$HOME/Library/Application Support/$instance_id" ;;
+    *)      app_data="${XDG_DATA_HOME:-$HOME/.local/share}/$instance_id" ;;
+esac
+
+pids_dir="$app_data/agents/agent-pids"
+[[ -d "$pids_dir" ]] || exit 0
+
+shopt -s nullglob
+pgids=()
+for pid_file in "$pids_dir"/*.pid; do
+    pgid="$(<"$pid_file")"
+    pgid="${pgid//[$'\t\r\n ']/}"
+    [[ "$pgid" =~ ^[0-9]+$ ]] || continue
+    pgids+=("$pgid")
+done
+[[ ${#pgids[@]} -gt 0 ]] || exit 0
+
+# SIGTERM the whole group first, give it a moment, then SIGKILL survivors.
+# `kill -- -<pgid>` targets the process group. Failures are expected and fine
+# (already-dead group, recycled PGID owned by someone else we can't signal).
+for pgid in "${pgids[@]}"; do
+    kill -TERM -- "-$pgid" 2>/dev/null || true
+done
+sleep 0.2
+for pgid in "${pgids[@]}"; do
+    kill -KILL -- "-$pgid" 2>/dev/null || true
+done