diff --git a/warehouse/query-core/src/main/java/datawave/core/iterators/DatawaveFieldIndexCachingIteratorJexl.java b/warehouse/query-core/src/main/java/datawave/core/iterators/DatawaveFieldIndexCachingIteratorJexl.java
index 9d7b8a4875..e3af3acc8f 100644
--- a/warehouse/query-core/src/main/java/datawave/core/iterators/DatawaveFieldIndexCachingIteratorJexl.java
+++ b/warehouse/query-core/src/main/java/datawave/core/iterators/DatawaveFieldIndexCachingIteratorJexl.java
@@ -367,6 +367,9 @@ public B withIvaratorSourcePool(GenericObjectPool<SortedKeyValueIterator<Key,Val
     // timeout for the building of the cache. Default 1 hour
     private volatile long scanTimeout = 1000L * 60 * 60;
 
+    // have we timed out
+    private volatile boolean timedOut = false;
+
     // The max number of results that can be returned from this iterator.
     private final long maxResults;
 
@@ -834,6 +837,14 @@ else if (key.compareTo(this.lastRangeSeeked.getStartKey()) < 0) {
 
                 if (this.setControl.isCancelledQuery()) {
                     this.topKey = null;
+                }
+
+                if (isTimedOut()) {
+                    log.error("Ivarator query timed out");
+                    throw new IvaratorException("Ivarator query timed out");
+                }
+
+                if (this.setControl.isCancelledQuery()) {
                     log.debug("Ivarator query was cancelled");
                     throw new IterationInterruptedException("Ivarator query was cancelled");
                 }
@@ -849,9 +860,15 @@ else if (key.compareTo(this.lastRangeSeeked.getStartKey()) < 0) {
             }
 
             if (this.setControl.isCancelledQuery()) {
-                log.debug("Ivarator query was cancelled");
-                throw new IterationInterruptedException("Ivarator query was cancelled");
+                if (isTimedOut()) {
+                    log.error("Ivarator query timed out");
+                    throw new IvaratorException("Ivarator query timed out");
+                } else {
+                    log.debug("Ivarator query was cancelled");
+                    throw new IterationInterruptedException("Ivarator query was cancelled");
+                }
             }
+
         }
     }
 
@@ -933,6 +950,8 @@ private void fillSortedSets() throws IOException {
         try {
             // wait for all of the threads to complete
             for (IvaratorFuture future : futures) {
+                checkTiming();
+
                 if (!failed && !this.setControl.isCancelledQuery()) {
                     try {
                         result = future.get(this.waitWindowObserver.remainingTimeMs(), TimeUnit.MILLISECONDS);
@@ -950,6 +969,9 @@ private void fillSortedSets() throws IOException {
                         this.setControl.setCancelled();
                     }
                 }
+                if (this.setControl.isCancelledQuery()) {
+                    break;
+                }
             }
         } finally {
             if (yieldKey == null) {
@@ -1035,6 +1057,27 @@ protected void startTiming() {
         startTime = System.currentTimeMillis();
     }
 
+    /**
+     * Check if the scan timeout has been reached. Mark as timed out and cancel the query if so.
+     */
+    protected void checkTiming() {
+        if (System.currentTimeMillis() > (startTime + scanTimeout)) {
+            // mark as timed out
+            this.timedOut = true;
+            // and cancel the query
+            this.setControl.setCancelled();
+        }
+    }
+
+    /**
+     * Was the timed out flag set.
+     *
+     * @return a boolean if timed out
+     */
+    protected boolean isTimedOut() {
+        return this.timedOut;
+    }
+
     /**
      * Get a source copy. This is only used when retrieving unsorted values.
      *
@@ -1184,6 +1227,8 @@ protected IvaratorFuture fillSet(final Range boundingFiRange, final TotalResults
                                 : null;
 
                 while (source.hasTop()) {
+                    checkTiming();
+
                     Key top = source.getTopKey();
 
                     // if we are setup for composite seeking, seek if we are out of range
@@ -1355,6 +1400,7 @@ protected boolean copyRowBasedHdfsBackedSetFromPreviousCall() {
         this.threadSafeSet = previousIvarator.threadSafeSet;
         this.set = previousIvarator.set;
         this.setControl = previousIvarator.setControl;
+        this.startTime = previousIvarator.startTime;
         return true;
     }
 
diff --git a/warehouse/query-core/src/main/java/datawave/core/iterators/IteratorThreadPoolManager.java b/warehouse/query-core/src/main/java/datawave/core/iterators/IteratorThreadPoolManager.java
index a183c3b795..944f84aed7 100644
--- a/warehouse/query-core/src/main/java/datawave/core/iterators/IteratorThreadPoolManager.java
+++ b/warehouse/query-core/src/main/java/datawave/core/iterators/IteratorThreadPoolManager.java
@@ -98,7 +98,7 @@ private IteratorThreadPoolManager(IteratorEnvironment env) {
                     DatawaveFieldIndexCachingIteratorJexl ivarator = future.getIvarator();
                     long elapsed = now - ivarator.getStartTime();
                     long ivaratorScanTimeout = ivarator.getScanTimeout();
-                    if (!ivarator.isRunning() && ((elapsed > ivaratorScanTimeout) || (elapsed > ivaratorMaxScanTimeout))) {
+                    if (ivarator.isRunning() && ((elapsed > ivaratorScanTimeout) || (elapsed > ivaratorMaxScanTimeout))) {
                         removeIvaratorFuture(taskName, env);
                     }
                 }