diff --git a/nifi-system-tests/nifi-stateless-system-test-suite/src/test/java/org/apache/nifi/stateless/basics/AsyncCommitCallbackIT.java b/nifi-system-tests/nifi-stateless-system-test-suite/src/test/java/org/apache/nifi/stateless/basics/AsyncCommitCallbackIT.java
index 2006a0ecd9..bf15b0629e 100644
--- a/nifi-system-tests/nifi-stateless-system-test-suite/src/test/java/org/apache/nifi/stateless/basics/AsyncCommitCallbackIT.java
+++ b/nifi-system-tests/nifi-stateless-system-test-suite/src/test/java/org/apache/nifi/stateless/basics/AsyncCommitCallbackIT.java
@@ -177,7 +177,11 @@ public class AsyncCommitCallbackIT extends StatelessSystemIT {
         Thread.sleep(1000L);
         assertFalse(trigger.getResultNow().isPresent());
 
-        Files.write(replacementFile.toPath(), "Good-bye World".getBytes(), StandardOpenOption.CREATE);
+        // Write to a temp file, then rename to the replacement file. Otherwise, the file may be created, and then the flow
+        // run before the data is written to the file, which can cause the FlowFile to be replaced with 0 bytes.
+        final File tempFile = new File(replacementFile.getParentFile(), "." + replacementFile.getName());
+        Files.write(tempFile.toPath(), "Good-bye World".getBytes(), StandardOpenOption.CREATE);
+        assertTrue(tempFile.renameTo(replacementFile));
 
         assertTrue(inputFile.exists());
 
diff --git a/nifi-system-tests/nifi-system-test-suite/src/test/java/org/apache/nifi/tests/system/processor/DynamicClassPathModificationIT.java b/nifi-system-tests/nifi-system-test-suite/src/test/java/org/apache/nifi/tests/system/processor/DynamicClassPathModificationIT.java
index a5561e40bf..1daa76d15d 100644
--- a/nifi-system-tests/nifi-system-test-suite/src/test/java/org/apache/nifi/tests/system/processor/DynamicClassPathModificationIT.java
+++ b/nifi-system-tests/nifi-system-test-suite/src/test/java/org/apache/nifi/tests/system/processor/DynamicClassPathModificationIT.java
@@ -149,8 +149,20 @@ public class DynamicClassPathModificationIT extends NiFiSystemIT {
         getNifiClient().getProcessorClient().terminateProcessor(modify.getId());
         getClientUtil().waitForStoppedProcessor(modify.getId());
 
-        // Empty the queue and generate another FlowFile with a sleep of 0 sec
+        // Empty the queue. Because the processor was terminated, it may still hold the FlowFile for a bit until the terminate completes.
+        // Because of that we'll wait until the queue is empty, attempting to empty it if it is not.
         getClientUtil().emptyQueue(modifyInputConnection.getId());
+        waitFor(() -> {
+            final int queueSize = getConnectionQueueSize(modifyInputConnection.getId());
+            if (queueSize == 0) {
+                return true;
+            }
+
+            getClientUtil().emptyQueue(modifyInputConnection.getId());
+            return false;
+        });
+
+        // Generate another FlowFile with a sleep of 0 sec
         getClientUtil().stopProcessor(generate);
         getClientUtil().updateProcessorProperties(generate, Collections.singletonMap("sleep", "0 sec"));
         getClientUtil().waitForValidProcessor(generate.getId());