diff --git a/buildSrc/src/main/java/org/elasticsearch/gradle/testclusters/ElasticsearchNode.java b/buildSrc/src/main/java/org/elasticsearch/gradle/testclusters/ElasticsearchNode.java
index 2f258733e7575..f43f28190da1a 100644
--- a/buildSrc/src/main/java/org/elasticsearch/gradle/testclusters/ElasticsearchNode.java
+++ b/buildSrc/src/main/java/org/elasticsearch/gradle/testclusters/ElasticsearchNode.java
@@ -807,6 +807,7 @@ public synchronized void stop(boolean tailLogs) {
         requireNonNull(esProcess, "Can't stop `" + this + "` as it was not started or already stopped.");
         // Test clusters are not reused, don't spend time on a graceful shutdown
         stopHandle(esProcess.toHandle(), true);
+        reaper.unregister(toString());
         if (tailLogs) {
             logFileContents("Standard output of node", esStdoutFile);
             logFileContents("Standard error of node", esStderrFile);
@@ -831,39 +832,43 @@ public void setNameCustomization(Function<String, String> nameCustomizer) {
     }
 
     private void stopHandle(ProcessHandle processHandle, boolean forcibly) {
-        // Stop all children first, ES could actually be a child when there's some wrapper process like on Windows.
+        // No-op if the process has already exited by itself.
         if (processHandle.isAlive() == false) {
             LOGGER.info("Process was not running when we tried to terminate it.");
             return;
         }
 
-        // Stop all children first, ES could actually be a child when there's some wrapper process like on Windows.
-        processHandle.children().forEach(each -> stopHandle(each, forcibly));
+        // Stop all children last - if the ML processes are killed before the ES JVM then
+        // they'll be recorded as having failed and won't restart when the cluster restarts.
+        // ES could actually be a child when there's some wrapper process like on Windows,
+        // and in that case the ML processes will be grandchildren of the wrapper.
+        List<ProcessHandle> children = processHandle.children().collect(Collectors.toList());
+        try {
+            logProcessInfo(
+                "Terminating elasticsearch process" + (forcibly ? " forcibly " : "gracefully") + ":",
+                processHandle.info()
+            );
 
-        logProcessInfo(
-            "Terminating elasticsearch process" + (forcibly ? " forcibly " : "gracefully") + ":",
-            processHandle.info()
-        );
+            if (forcibly) {
+                processHandle.destroyForcibly();
+            } else {
+                processHandle.destroy();
+                waitForProcessToExit(processHandle);
+                if (processHandle.isAlive() == false) {
+                    return;
+                }
+                LOGGER.info("process did not terminate after {} {}, stopping it forcefully",
+                    ES_DESTROY_TIMEOUT, ES_DESTROY_TIMEOUT_UNIT);
+                processHandle.destroyForcibly();
+            }
 
-        if (forcibly) {
-            processHandle.destroyForcibly();
-        } else {
-            processHandle.destroy();
             waitForProcessToExit(processHandle);
-            if (processHandle.isAlive() == false) {
-                return;
+            if (processHandle.isAlive()) {
+                throw new TestClustersException("Was not able to terminate elasticsearch process for " + this);
             }
-            LOGGER.info("process did not terminate after {} {}, stopping it forcefully",
-                ES_DESTROY_TIMEOUT, ES_DESTROY_TIMEOUT_UNIT);
-            processHandle.destroyForcibly();
-        }
-
-        waitForProcessToExit(processHandle);
-        if (processHandle.isAlive()) {
-            throw new TestClustersException("Was not able to terminate elasticsearch process for " + this);
+        } finally {
+            children.forEach(each -> stopHandle(each, forcibly));
         }
-
-        reaper.unregister(toString());
     }
 
     private void logProcessInfo(String prefix, ProcessHandle.Info info) {
diff --git a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MlMappingsUpgradeIT.java b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MlMappingsUpgradeIT.java
index 8099812c8ea1b..13ed2dafc5f31 100644
--- a/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MlMappingsUpgradeIT.java
+++ b/x-pack/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/MlMappingsUpgradeIT.java
@@ -38,7 +38,6 @@ protected Collection<String> templatesToWaitFor() {
      * The purpose of this test is to ensure that when a job is open through a rolling upgrade we upgrade the results
      * index mappings when it is assigned to an upgraded node even if no other ML endpoint is called after the upgrade
      */
-    @AwaitsFix(bugUrl = "https://github.com/elastic/elasticsearch/issues/46262")
     public void testMappingsUpgrade() throws Exception {
 
         switch (CLUSTER_TYPE) {