diff --git a/src/interfaces/node.cpp b/src/interfaces/node.cpp
--- a/src/interfaces/node.cpp
+++ b/src/interfaces/node.cpp
@@ -89,7 +89,15 @@
             Interrupt(*m_context);
             Shutdown(*m_context);
         }
-        void startShutdown() override { StartShutdown(); }
+        void startShutdown() override {
+            StartShutdown();
+            // Stop RPC for clean shutdown if any of waitfor* commands is
+            // executed.
+            if (gArgs.GetBoolArg("-server", false)) {
+                InterruptRPC();
+                StopRPC();
+            }
+        }
         bool shutdownRequested() override { return ShutdownRequested(); }
         void mapPort(bool use_upnp) override {
             if (use_upnp) {
diff --git a/src/rpc/server.cpp b/src/rpc/server.cpp
--- a/src/rpc/server.cpp
+++ b/src/rpc/server.cpp
@@ -16,12 +16,16 @@
 #include <boost/algorithm/string/split.hpp>
 #include <boost/signals2/signal.hpp>
 
+#include <cassert>
 #include <memory> // for unique_ptr
+#include <mutex>
 #include <set>
 #include <unordered_map>
 
 static RecursiveMutex cs_rpcWarmup;
 static std::atomic<bool> g_rpc_running{false};
+static std::once_flag g_rpc_interrupt_flag;
+static std::once_flag g_rpc_stop_flag;
 static bool fRPCInWarmup GUARDED_BY(cs_rpcWarmup) = true;
 static std::string
     rpcWarmupStatus GUARDED_BY(cs_rpcWarmup) = "RPC server started";
@@ -343,16 +347,25 @@
 }
 
 void InterruptRPC() {
-    LogPrint(BCLog::RPC, "Interrupting RPC\n");
-    // Interrupt e.g. running longpolls
-    g_rpc_running = false;
+    // This function could be called twice if the GUI has been started with
+    // -server=1.
+    std::call_once(g_rpc_interrupt_flag, []() {
+        LogPrint(BCLog::RPC, "Interrupting RPC\n");
+        // Interrupt e.g. running longpolls
+        g_rpc_running = false;
+    });
 }
 
 void StopRPC() {
-    LogPrint(BCLog::RPC, "Stopping RPC\n");
-    WITH_LOCK(g_deadline_timers_mutex, deadlineTimers.clear());
-    DeleteAuthCookie();
-    g_rpcSignals.Stopped();
+    // This function could be called twice if the GUI has been started with
+    // -server=1.
+    assert(!g_rpc_running);
+    std::call_once(g_rpc_stop_flag, []() {
+        LogPrint(BCLog::RPC, "Stopping RPC\n");
+        WITH_LOCK(g_deadline_timers_mutex, deadlineTimers.clear());
+        DeleteAuthCookie();
+        g_rpcSignals.Stopped();
+    });
 }
 
 bool IsRPCRunning() {