diff --git a/server/src/main/java/org/elasticsearch/index/engine/NoOpEngine.java b/server/src/main/java/org/elasticsearch/index/engine/NoOpEngine.java
index 89dee26cc2895..06520d3036c31 100644
--- a/server/src/main/java/org/elasticsearch/index/engine/NoOpEngine.java
+++ b/server/src/main/java/org/elasticsearch/index/engine/NoOpEngine.java
@@ -54,7 +54,8 @@ public NoOpEngine(EngineConfig config) {
         super(config, null, null, true, Function.identity());
         this.stats = new SegmentsStats();
         Directory directory = store.directory();
-        try (DirectoryReader reader = openDirectory(directory, config.getIndexSettings())) {
+        // Do not wrap soft-deletes reader when calculating segment stats as the wrapper might filter out fully deleted segments.
+        try (DirectoryReader reader = openDirectory(directory, false)) {
             for (LeafReaderContext ctx : reader.getContext().leaves()) {
                 SegmentReader segmentReader = Lucene.segmentReader(ctx.reader());
                 fillSegmentStats(segmentReader, true, stats);
diff --git a/server/src/main/java/org/elasticsearch/index/engine/ReadOnlyEngine.java b/server/src/main/java/org/elasticsearch/index/engine/ReadOnlyEngine.java
index c294e5dd732b4..2ffdcb71425eb 100644
--- a/server/src/main/java/org/elasticsearch/index/engine/ReadOnlyEngine.java
+++ b/server/src/main/java/org/elasticsearch/index/engine/ReadOnlyEngine.java
@@ -33,7 +33,6 @@
 import org.elasticsearch.common.lucene.index.ElasticsearchDirectoryReader;
 import org.elasticsearch.common.util.concurrent.ReleasableLock;
 import org.elasticsearch.core.internal.io.IOUtils;
-import org.elasticsearch.index.IndexSettings;
 import org.elasticsearch.index.mapper.MapperService;
 import org.elasticsearch.index.seqno.SeqNoStats;
 import org.elasticsearch.index.seqno.SequenceNumbers;
@@ -536,9 +535,9 @@ public void advanceMaxSeqNoOfUpdatesOrDeletes(long maxSeqNoOfUpdatesOnPrimary) {
             maxSeqNoOfUpdatesOnPrimary + ">" + getMaxSeqNoOfUpdatesOrDeletes();
     }
 
-    protected DirectoryReader openDirectory(Directory dir, IndexSettings indexSettings) throws IOException {
-        final DirectoryReader reader = DirectoryReader.open(dir, OFF_HEAP_READER_ATTRIBUTES);
-        if (indexSettings.isSoftDeleteEnabled()) {
+    protected static DirectoryReader openDirectory(Directory directory, boolean wrapSoftDeletes) throws IOException {
+        final DirectoryReader reader = DirectoryReader.open(directory, OFF_HEAP_READER_ATTRIBUTES);
+        if (wrapSoftDeletes) {
             return new SoftDeletesDirectoryReaderWrapper(reader, Lucene.SOFT_DELETES_FIELD);
         } else {
             return reader;
diff --git a/x-pack/plugin/frozen-indices/src/main/java/org/elasticsearch/index/engine/FrozenEngine.java b/x-pack/plugin/frozen-indices/src/main/java/org/elasticsearch/index/engine/FrozenEngine.java
index 05b6054837c82..ba57fa827a88e 100644
--- a/x-pack/plugin/frozen-indices/src/main/java/org/elasticsearch/index/engine/FrozenEngine.java
+++ b/x-pack/plugin/frozen-indices/src/main/java/org/elasticsearch/index/engine/FrozenEngine.java
@@ -21,6 +21,7 @@
 import org.apache.lucene.index.PointValues;
 import org.apache.lucene.index.SegmentCommitInfo;
 import org.apache.lucene.index.SegmentReader;
+import org.apache.lucene.index.SoftDeletesDirectoryReaderWrapper;
 import org.apache.lucene.index.SortedDocValues;
 import org.apache.lucene.index.SortedNumericDocValues;
 import org.apache.lucene.index.SortedSetDocValues;
@@ -77,9 +78,8 @@ public FrozenEngine(EngineConfig config) {
 
         boolean success = false;
         Directory directory = store.directory();
-        try (DirectoryReader reader = openDirectory(directory, config.getIndexSettings())) {
-            canMatchReader = ElasticsearchDirectoryReader.wrap(new RewriteCachingDirectoryReader(directory, reader.leaves()),
-                config.getShardId());
+        // Do not wrap soft-deletes reader when calculating segment stats as the wrapper might filter out fully deleted segments.
+        try (DirectoryReader reader = openDirectory(directory, false)) {
             // we record the segment stats here - that's what the reader needs when it's open and it give the user
             // an idea of what it can save when it's closed
             this.stats = new SegmentsStats();
@@ -87,6 +87,10 @@ public FrozenEngine(EngineConfig config) {
                 SegmentReader segmentReader = Lucene.segmentReader(ctx.reader());
                 fillSegmentStats(segmentReader, true, stats);
             }
+            final DirectoryReader wrappedReader = config.getIndexSettings().isSoftDeleteEnabled() ?
+                new SoftDeletesDirectoryReaderWrapper(reader, Lucene.SOFT_DELETES_FIELD) : reader;
+            canMatchReader = ElasticsearchDirectoryReader.wrap(
+                new RewriteCachingDirectoryReader(directory, wrappedReader.leaves()), config.getShardId());
             success = true;
         } catch (IOException e) {
             throw new UncheckedIOException(e);
@@ -167,7 +171,8 @@ private synchronized ElasticsearchDirectoryReader getOrOpenReader() throws IOExc
                 for (ReferenceManager.RefreshListener listeners : config ().getInternalRefreshListener()) {
                     listeners.beforeRefresh();
                 }
-                final DirectoryReader dirReader = openDirectory(engineConfig.getStore().directory(), engineConfig.getIndexSettings());
+                final DirectoryReader dirReader = openDirectory(engineConfig.getStore().directory(),
+                    engineConfig.getIndexSettings().isSoftDeleteEnabled());
                 reader = lastOpenedReader = wrapReader(dirReader, Function.identity());
                 processReader(reader);
                 reader.getReaderCacheHelper().addClosedListener(this::onReaderClosed);