diff --git a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/DataFrameAnalyticsManager.java b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/DataFrameAnalyticsManager.java
index aa84fda1f70..a096eae3345 100644
--- a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/DataFrameAnalyticsManager.java
+++ b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/DataFrameAnalyticsManager.java
@@ -90,10 +90,7 @@ public class DataFrameAnalyticsManager {
         // With config in hand, determine action to take
         ActionListener<DataFrameAnalyticsConfig> configListener = ActionListener.wrap(
             config -> {
-                // At this point we have the config at hand and we can reset the progress tracker
-                // to use the analyses phases. We preserve reindexing progress as if reindexing was
-                // finished it will not be reset.
-                task.getStatsHolder().resetProgressTrackerPreservingReindexingProgress(config.getAnalysis().getProgressPhases(),
+                task.getStatsHolder().adjustProgressTracker(config.getAnalysis().getProgressPhases(),
                     config.getAnalysis().supportsInference());
 
                 switch(currentState) {
diff --git a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolder.java b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolder.java
index 2adb206a5d0..0ae94d9b624 100644
--- a/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolder.java
+++ b/x-pack/plugin/ml/src/main/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolder.java
@@ -30,10 +30,14 @@ public class StatsHolder {
         dataCountsTracker = new DataCountsTracker();
     }
 
-    public void resetProgressTrackerPreservingReindexingProgress(List<String> analysisPhases, boolean hasInferencePhase) {
+    public void adjustProgressTracker(List<String> analysisPhases, boolean hasInferencePhase) {
         int reindexingProgressPercent = progressTracker.getReindexingProgressPercent();
         progressTracker = ProgressTracker.fromZeroes(analysisPhases, hasInferencePhase);
-        progressTracker.updateReindexingProgress(reindexingProgressPercent);
+
+        // If reindexing progress was less than 100 (ie not complete) we reset it to 1
+        // as we will have to do reindexing from scratch and at the same time we want
+        // to differentiate from a job that has never started before.
+        progressTracker.updateReindexingProgress(reindexingProgressPercent < 100 ? 1 : reindexingProgressPercent);
     }
 
     public ProgressTracker getProgressTracker() {
diff --git a/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolderTests.java b/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolderTests.java
index f71afeabced..d321da67deb 100644
--- a/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolderTests.java
+++ b/x-pack/plugin/ml/src/test/java/org/elasticsearch/xpack/ml/dataframe/stats/StatsHolderTests.java
@@ -19,10 +19,10 @@ import static org.hamcrest.Matchers.equalTo;
 
 public class StatsHolderTests extends ESTestCase {
 
-    public void testResetProgressTrackerPreservingReindexingProgress_GivenSameAnalysisPhases() {
+    public void testAdjustProgressTracker_GivenSameAnalysisPhases() {
         List<PhaseProgress> phases = Collections.unmodifiableList(
             Arrays.asList(
-                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("reindexing", 10),
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("reindexing", 100),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("loading_data", 20),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("a", 30),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("b", 40),
@@ -31,24 +31,24 @@ public class StatsHolderTests extends ESTestCase {
         );
         StatsHolder statsHolder = new StatsHolder(phases);
 
-        statsHolder.resetProgressTrackerPreservingReindexingProgress(Arrays.asList("a", "b"), false);
+        statsHolder.adjustProgressTracker(Arrays.asList("a", "b"), false);
 
         List<PhaseProgress> phaseProgresses = statsHolder.getProgressTracker().report();
 
         assertThat(phaseProgresses.size(), equalTo(5));
         assertThat(phaseProgresses.stream().map(PhaseProgress::getPhase).collect(Collectors.toList()),
             contains("reindexing", "loading_data", "a", "b", "writing_results"));
-        assertThat(phaseProgresses.get(0).getProgressPercent(), equalTo(10));
+        assertThat(phaseProgresses.get(0).getProgressPercent(), equalTo(100));
         assertThat(phaseProgresses.get(1).getProgressPercent(), equalTo(0));
         assertThat(phaseProgresses.get(2).getProgressPercent(), equalTo(0));
         assertThat(phaseProgresses.get(3).getProgressPercent(), equalTo(0));
         assertThat(phaseProgresses.get(4).getProgressPercent(), equalTo(0));
     }
 
-    public void testResetProgressTrackerPreservingReindexingProgress_GivenDifferentAnalysisPhases() {
+    public void testAdjustProgressTracker_GivenDifferentAnalysisPhases() {
         List<PhaseProgress> phases = Collections.unmodifiableList(
             Arrays.asList(
-                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("reindexing", 10),
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("reindexing", 100),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("loading_data", 20),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("a", 30),
                 new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("b", 40),
@@ -57,14 +57,40 @@ public class StatsHolderTests extends ESTestCase {
         );
         StatsHolder statsHolder = new StatsHolder(phases);
 
-        statsHolder.resetProgressTrackerPreservingReindexingProgress(Arrays.asList("c", "d"), false);
+        statsHolder.adjustProgressTracker(Arrays.asList("c", "d"), false);
 
         List<PhaseProgress> phaseProgresses = statsHolder.getProgressTracker().report();
 
         assertThat(phaseProgresses.size(), equalTo(5));
         assertThat(phaseProgresses.stream().map(PhaseProgress::getPhase).collect(Collectors.toList()),
             contains("reindexing", "loading_data", "c", "d", "writing_results"));
-        assertThat(phaseProgresses.get(0).getProgressPercent(), equalTo(10));
+        assertThat(phaseProgresses.get(0).getProgressPercent(), equalTo(100));
+        assertThat(phaseProgresses.get(1).getProgressPercent(), equalTo(0));
+        assertThat(phaseProgresses.get(2).getProgressPercent(), equalTo(0));
+        assertThat(phaseProgresses.get(3).getProgressPercent(), equalTo(0));
+        assertThat(phaseProgresses.get(4).getProgressPercent(), equalTo(0));
+    }
+
+    public void testAdjustProgressTracker_GivenReindexingProgressIncomplete() {
+        List<PhaseProgress> phases = Collections.unmodifiableList(
+            Arrays.asList(
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("reindexing", 42),
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("loading_data", 20),
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("a", 30),
+                new org.elasticsearch.xpack.core.ml.utils.PhaseProgress("b", 40),
+                new PhaseProgress("writing_results", 50)
+            )
+        );
+        StatsHolder statsHolder = new StatsHolder(phases);
+
+        statsHolder.adjustProgressTracker(Arrays.asList("a", "b"), false);
+
+        List<PhaseProgress> phaseProgresses = statsHolder.getProgressTracker().report();
+
+        assertThat(phaseProgresses.size(), equalTo(5));
+        assertThat(phaseProgresses.stream().map(PhaseProgress::getPhase).collect(Collectors.toList()),
+            contains("reindexing", "loading_data", "a", "b", "writing_results"));
+        assertThat(phaseProgresses.get(0).getProgressPercent(), equalTo(1));
         assertThat(phaseProgresses.get(1).getProgressPercent(), equalTo(0));
         assertThat(phaseProgresses.get(2).getProgressPercent(), equalTo(0));
         assertThat(phaseProgresses.get(3).getProgressPercent(), equalTo(0));