diff --git a/.github/workflows/nightly-e2e.yaml b/.github/workflows/nightly-e2e.yaml
index c8af228b4a5..e0b8bc776e8 100644
--- a/.github/workflows/nightly-e2e.yaml
+++ b/.github/workflows/nightly-e2e.yaml
@@ -806,7 +806,7 @@ jobs:
        inputs.jobs == '' ||
        contains(format(',{0},', inputs.jobs), ',double-onboard-e2e,'))
     runs-on: ubuntu-latest
-    timeout-minutes: 60
+    timeout-minutes: 90
     steps:
       - name: Checkout
         uses: actions/checkout@v6
diff --git a/test/e2e/test-double-onboard.sh b/test/e2e/test-double-onboard.sh
index acf17d5f017..2721d753960 100755
--- a/test/e2e/test-double-onboard.sh
+++ b/test/e2e/test-double-onboard.sh
@@ -40,6 +40,33 @@ section() {
 }
 info() { printf '\033[1;34m  [info]\033[0m %s\n' "$1"; }
 
+# TODO(#2562): replace shell timeout with structured timeout once unified abstraction lands
+
+# Per-phase timeout in seconds (20 min per onboard phase, generous for CI)
+PHASE_TIMEOUT="${NEMOCLAW_E2E_PHASE_TIMEOUT:-1200}"
+
+# Elapsed-time helpers
+phase_start_time() { date +%s; }
+phase_elapsed() {
+  local start="$1"
+  local now
+  now="$(date +%s)"
+  echo $((now - start))
+}
+
+# Diagnostic dump — called on phase timeout or failure to aid debugging
+dump_diagnostics() {
+  local phase_label="${1:-unknown}"
+  info "=== Diagnostics for ${phase_label} ==="
+  info "openshell status:"
+  openshell status 2>&1 | sed 's/^/    /' || true
+  info "openshell sandbox list:"
+  openshell sandbox list 2>&1 | sed 's/^/    /' || true
+  info "docker ps:"
+  docker ps 2>&1 | sed 's/^/    /' || true
+  info "=== End diagnostics ==="
+}
+
 registry_has() {
   local sandbox_name="$1"
   [ -f "$REGISTRY" ] && grep -q "$sandbox_name" "$REGISTRY"
@@ -141,6 +168,7 @@ PY
   return 1
 }
 
+# TODO(#2562): replace shell timeout with structured timeout once unified abstraction lands
 run_onboard() {
   local sandbox_name="$1"
   local recreate="${2:-0}"
@@ -161,7 +189,7 @@ run_onboard() {
     env_args+=("NEMOCLAW_RECREATE_SANDBOX=1")
   fi
 
-  env "${env_args[@]}" "${NEMOCLAW_CMD[@]}" onboard --non-interactive >"$log_file" 2>&1
+  run_with_timeout "$PHASE_TIMEOUT" env "${env_args[@]}" "${NEMOCLAW_CMD[@]}" onboard --non-interactive >"$log_file" 2>&1
   RUN_ONBOARD_EXIT=$?
   RUN_ONBOARD_OUTPUT="$(cat "$log_file")"
   rm -f "$log_file"
@@ -234,14 +262,20 @@ fi
 section "Phase 2: First onboard ($SANDBOX_A)"
 info "Running successful non-interactive onboard against local compatible endpoint..."
 
+PHASE2_START="$(phase_start_time)"
 run_onboard "$SANDBOX_A"
 output1="$RUN_ONBOARD_OUTPUT"
 exit1="$RUN_ONBOARD_EXIT"
+info "Phase 2 elapsed: $(phase_elapsed "$PHASE2_START")s"
 
 if [ "$exit1" -eq 0 ]; then
   pass "First onboard completed successfully"
+elif [ "$exit1" -eq 124 ]; then
+  fail "First onboard timed out after ${PHASE_TIMEOUT}s (exit 124)"
+  dump_diagnostics "Phase 2"
 else
   fail "First onboard exited $exit1 (expected 0)"
+  dump_diagnostics "Phase 2"
 fi
 
 if grep -q "Sandbox '${SANDBOX_A}' created" <<<"$output1"; then
@@ -274,17 +308,23 @@ fi
 section "Phase 3: Second onboard ($SANDBOX_A — same name, recreate)"
 info "Running nemoclaw onboard with NEMOCLAW_RECREATE_SANDBOX=1..."
 
+PHASE3_START="$(phase_start_time)"
 run_onboard "$SANDBOX_A" "1"
 output2="$RUN_ONBOARD_OUTPUT"
 exit2="$RUN_ONBOARD_EXIT"
+info "Phase 3 elapsed: $(phase_elapsed "$PHASE3_START")s"
 
 if [ "$exit2" -eq 0 ]; then
   pass "Second onboard completed successfully"
+elif [ "$exit2" -eq 124 ]; then
+  fail "Second onboard timed out after ${PHASE_TIMEOUT}s (exit 124)"
+  dump_diagnostics "Phase 3"
 else
   fail "Second onboard exited $exit2 (expected 0)"
+  dump_diagnostics "Phase 3"
 fi
 
-if grep -q "Reusing existing NemoClaw gateway" <<<"$output2"; then
+if grep -q "Reusing healthy NemoClaw gateway" <<<"$output2"; then
   pass "Healthy gateway reused on second onboard"
 else
   fail "Healthy gateway was not reused on second onboard"
@@ -314,17 +354,23 @@ fi
 section "Phase 4: Third onboard ($SANDBOX_B — different name)"
 info "Running nemoclaw onboard with new sandbox name..."
 
+PHASE4_START="$(phase_start_time)"
 run_onboard "$SANDBOX_B"
 output3="$RUN_ONBOARD_OUTPUT"
 exit3="$RUN_ONBOARD_EXIT"
+info "Phase 4 elapsed: $(phase_elapsed "$PHASE4_START")s"
 
 if [ "$exit3" -eq 0 ]; then
   pass "Third onboard completed successfully"
+elif [ "$exit3" -eq 124 ]; then
+  fail "Third onboard timed out after ${PHASE_TIMEOUT}s (exit 124)"
+  dump_diagnostics "Phase 4"
 else
   fail "Third onboard exited $exit3 (expected 0)"
+  dump_diagnostics "Phase 4"
 fi
 
-if grep -q "Reusing existing NemoClaw gateway" <<<"$output3"; then
+if grep -q "Reusing healthy NemoClaw gateway" <<<"$output3"; then
   pass "Healthy gateway reused on third onboard"
 else
   fail "Healthy gateway was not reused on third onboard"
@@ -441,6 +487,13 @@ openshell sandbox delete "$SANDBOX_B" 2>/dev/null || true
 openshell forward stop 18789 2>/dev/null || true
 openshell gateway destroy -g nemoclaw 2>/dev/null || true
 
+# Force registry reconciliation: when the gateway is in a degraded state
+# (stopped in Phase 6), `nemoclaw destroy` may delete the sandbox from
+# OpenShell but fail to clean its own registry entry. Running `status` for
+# each sandbox triggers the stale-entry reconciliation path.
+run_nemoclaw "$SANDBOX_A" status 2>/dev/null || true
+run_nemoclaw "$SANDBOX_B" status 2>/dev/null || true
+
 if openshell sandbox get "$SANDBOX_A" >/dev/null 2>&1; then
   fail "Sandbox '$SANDBOX_A' still exists after cleanup"
 else