diff --git a/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpoint.java b/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpoint.java
index 81a06eb4524d1..69877c4cbe700 100644
--- a/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpoint.java
+++ b/x-pack/plugin/core/src/main/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpoint.java
@@ -279,28 +279,30 @@ public static long getBehind(DataFrameTransformCheckpoint oldCheckpoint, DataFra
             throw new IllegalArgumentException("old checkpoint is newer than new checkpoint");
         }
 
-        // get the sum of of shard checkpoints
+        // get the sum of of shard operations (that are fully replicated), which is 1 higher than the global checkpoint for each shard
         // note: we require shard checkpoints to strictly increase and never decrease
-        long oldCheckPointSum = 0;
-        long newCheckPointSum = 0;
+        long oldCheckPointOperationsSum = 0;
+        long newCheckPointOperationsSum = 0;
 
         for (Entry<String, long[]> entry : oldCheckpoint.indicesCheckpoints.entrySet()) {
             // ignore entries that aren't part of newCheckpoint, e.g. deleted indices
             if (newCheckpoint.indicesCheckpoints.containsKey(entry.getKey())) {
-                oldCheckPointSum += Arrays.stream(entry.getValue()).sum();
+                // Add 1 per shard as sequence numbers start at 0, i.e. sequence number 0 means there has been 1 operation
+                oldCheckPointOperationsSum += Arrays.stream(entry.getValue()).sum() + entry.getValue().length;
             }
         }
 
         for (long[] v : newCheckpoint.indicesCheckpoints.values()) {
-            newCheckPointSum += Arrays.stream(v).sum();
+            // Add 1 per shard as sequence numbers start at 0, i.e. sequence number 0 means there has been 1 operation
+            newCheckPointOperationsSum += Arrays.stream(v).sum() + v.length;
         }
 
         // this should not be possible
-        if (newCheckPointSum < oldCheckPointSum) {
+        if (newCheckPointOperationsSum < oldCheckPointOperationsSum) {
             return -1L;
         }
 
-        return newCheckPointSum - oldCheckPointSum;
+        return newCheckPointOperationsSum - oldCheckPointOperationsSum;
     }
 
     private static Map<String, long[]> readCheckpoints(Map<String, Object> readMap) {
diff --git a/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpointTests.java b/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpointTests.java
index 67cc4b91584c2..298b018ce453b 100644
--- a/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpointTests.java
+++ b/x-pack/plugin/core/src/test/java/org/elasticsearch/xpack/core/dataframe/transforms/DataFrameTransformCheckpointTests.java
@@ -106,7 +106,7 @@ public void testGetBehind() {
             List<Long> checkpoints2 = new ArrayList<>();
 
             for (int j = 0; j < shards; ++j) {
-                long shardCheckpoint = randomLongBetween(0, 1_000_000);
+                long shardCheckpoint = randomLongBetween(-1, 1_000_000);
                 checkpoints1.add(shardCheckpoint);
                 checkpoints2.add(shardCheckpoint + 10);
             }
@@ -152,11 +152,11 @@ public void testGetBehind() {
         assertEquals(-1L, DataFrameTransformCheckpoint.getBehind(checkpointOlderButNewerShardsCheckpoint, checkpointOld));
 
         // test cases where indices sets do not match
-        // remove something from old, so newer has 1 index more than old
+        // remove something from old, so newer has 1 index more than old: should be equivalent to old index existing but empty
         checkpointsByIndexOld.remove(checkpointsByIndexOld.firstKey());
         long behind = DataFrameTransformCheckpoint.getBehind(checkpointOld, checkpointTransientNew);
-        assertTrue("Expected behind (" + behind + ") > sum of shard checkpoints (" + indices * shards * 10L + ")",
-                behind > indices * shards * 10L);
+        assertTrue("Expected behind (" + behind + ") => sum of shard checkpoint differences (" + indices * shards * 10L + ")",
+                behind >= indices * shards * 10L);
 
         // remove same key: old and new should have equal indices again
         checkpointsByIndexNew.remove(checkpointsByIndexNew.firstKey());
diff --git a/x-pack/plugin/data-frame/src/main/java/org/elasticsearch/xpack/dataframe/checkpoint/DefaultCheckpointProvider.java b/x-pack/plugin/data-frame/src/main/java/org/elasticsearch/xpack/dataframe/checkpoint/DefaultCheckpointProvider.java
index 23b1bdde12b4f..5464304d5b8e0 100644
--- a/x-pack/plugin/data-frame/src/main/java/org/elasticsearch/xpack/dataframe/checkpoint/DefaultCheckpointProvider.java
+++ b/x-pack/plugin/data-frame/src/main/java/org/elasticsearch/xpack/dataframe/checkpoint/DefaultCheckpointProvider.java
@@ -183,8 +183,8 @@ static Map<String, long[]> extractIndexCheckPoints(ShardStats[] shards, Set<Stri
             String indexName = shard.getShardRouting().getIndexName();
 
             if (userIndices.contains(indexName)) {
-                // SeqNoStats could be `null`, assume the global checkpoint to be 0 in this case
-                long globalCheckpoint = shard.getSeqNoStats() == null ? 0 : shard.getSeqNoStats().getGlobalCheckpoint();
+                // SeqNoStats could be `null`, assume the global checkpoint to be -1 in this case
+                long globalCheckpoint = shard.getSeqNoStats() == null ? -1L : shard.getSeqNoStats().getGlobalCheckpoint();
                 if (checkpointsByIndex.containsKey(indexName)) {
                     // we have already seen this index, just check/add shards
                     TreeMap<Integer, Long> checkpoints = checkpointsByIndex.get(indexName);
@@ -215,8 +215,7 @@ static Map<String, long[]> extractIndexCheckPoints(ShardStats[] shards, Set<Stri
 
             userIndicesClone.removeAll(checkpointsByIndex.keySet());
             if (userIndicesClone.isEmpty() == false) {
-                logger.debug("Original set of user indices contained more indexes [{}]",
-                        userIndicesClone);
+                logger.debug("Original set of user indices contained more indexes [{}]", userIndicesClone);
             }
         }
 
diff --git a/x-pack/plugin/data-frame/src/test/java/org/elasticsearch/xpack/dataframe/checkpoint/DataFrameTransformsCheckpointServiceTests.java b/x-pack/plugin/data-frame/src/test/java/org/elasticsearch/xpack/dataframe/checkpoint/DataFrameTransformsCheckpointServiceTests.java
index 1947e7b1d064d..8a9a5bd50af92 100644
--- a/x-pack/plugin/data-frame/src/test/java/org/elasticsearch/xpack/dataframe/checkpoint/DataFrameTransformsCheckpointServiceTests.java
+++ b/x-pack/plugin/data-frame/src/test/java/org/elasticsearch/xpack/dataframe/checkpoint/DataFrameTransformsCheckpointServiceTests.java
@@ -184,7 +184,7 @@ private static ShardStats[] createRandomShardStats(Map<String, long[]> expectedC
 
                 // add broken seqNoStats if requested
                 if (missingSeqNoStats && index.getName().equals(missingSeqNoStatsIndex)) {
-                    checkpoints.add(0L);
+                    checkpoints.add(-1L);
                 } else {
                     validSeqNoStats = new SeqNoStats(maxSeqNo, localCheckpoint, globalCheckpoint);
                     checkpoints.add(globalCheckpoint);