diff --git a/docs/changelog/112250.yaml b/docs/changelog/112250.yaml
new file mode 100644
index 000000000000..edbb5667d4b9
--- /dev/null
+++ b/docs/changelog/112250.yaml
@@ -0,0 +1,5 @@
+pr: 112250
+summary: Do not exclude empty arrays or empty objects in source filtering
+area: Search
+type: bug
+issues: [109668]
diff --git a/libs/x-content/impl/src/main/java/org/elasticsearch/xcontent/provider/filtering/FilterPathBasedFilter.java b/libs/x-content/impl/src/main/java/org/elasticsearch/xcontent/provider/filtering/FilterPathBasedFilter.java
index e0b5875c6c10..4562afa8af69 100644
--- a/libs/x-content/impl/src/main/java/org/elasticsearch/xcontent/provider/filtering/FilterPathBasedFilter.java
+++ b/libs/x-content/impl/src/main/java/org/elasticsearch/xcontent/provider/filtering/FilterPathBasedFilter.java
@@ -96,6 +96,41 @@ public class FilterPathBasedFilter extends TokenFilter {
         return filter;
     }
 
+    /**
+     * This is overridden in order to keep empty arrays in nested exclusions - see #109668.
+     * <p>
+     * If we are excluding contents, we only want to exclude based on property name - but empty arrays in themselves do not have a property
+     * name. If the empty array were to be excluded, it should be done by excluding the parent.
+     * <p>
+     * Note though that the expected behavior seems to be ambiguous if contentsFiltered is true - that is, that the filter has pruned all
+     * the contents of a given array, such that we are left with the empty array. The behavior below drops that array, for at the time of
+     * writing, not doing so would cause assertions in JsonXContentFilteringTests to fail, which expect this behavior. Yet it is not obvious
+     * if dropping the empty array in this case is correct. For example, one could expect this sort of behavior:
+     * <ul>
+     *     <li>Document: <pre>{ "myArray": [ { "myField": "myValue" } ]}</pre></li>
+     *     <li>Filter: <pre>{ "exclude": "myArray.myField" }</pre></li>
+     * </ul>
+     * From the user's perspective, this could reasonably yield either of:
+     * <ol>
+     *     <li><pre>{ "myArray": []}</pre></li>
+     *     <li>Removing {@code myArray} entirely.</li>
+     * </ol>
+     */
+    @Override
+    public boolean includeEmptyArray(boolean contentsFiltered) {
+        return inclusive == false && contentsFiltered == false;
+    }
+
+    /**
+     * This is overridden in order to keep empty objects in nested exclusions - see #109668.
+     * <p>
+     * The same logic applies to this as to {@link #includeEmptyArray(boolean)}, only for nested objects instead of nested arrays.
+     */
+    @Override
+    public boolean includeEmptyObject(boolean contentsFiltered) {
+        return inclusive == false && contentsFiltered == false;
+    }
+
     @Override
     protected boolean _includeScalar() {
         return inclusive == false;
diff --git a/server/src/test/java/org/elasticsearch/search/lookup/SourceFilterTests.java b/server/src/test/java/org/elasticsearch/search/lookup/SourceFilterTests.java
index 370584e3f29f..bddfd53b2b12 100644
--- a/server/src/test/java/org/elasticsearch/search/lookup/SourceFilterTests.java
+++ b/server/src/test/java/org/elasticsearch/search/lookup/SourceFilterTests.java
@@ -112,4 +112,48 @@ public class SourceFilterTests extends ESTestCase {
 
     }
 
+    // Verification for issue #109668
+    public void testIncludeParentAndExcludeChildEmptyArray() {
+        Source fromMap = Source.fromMap(Map.of("myArray", List.of()), XContentType.JSON);
+        Source filteredMap = fromMap.filter(new SourceFilter(new String[] { "myArray" }, new String[] { "myArray.myField" }));
+        assertEquals(filteredMap.source(), Map.of("myArray", List.of()));
+        Source fromBytes = Source.fromBytes(new BytesArray("{\"myArray\": []}"), XContentType.JSON);
+        Source filteredBytes = fromBytes.filter(new SourceFilter(new String[] { "myArray" }, new String[] { "myArray.myField" }));
+        assertEquals(filteredBytes.source(), Map.of("myArray", List.of()));
+    }
+
+    public void testIncludeParentAndExcludeChildEmptyObject() {
+        Source fromMap = Source.fromMap(Map.of("myObject", Map.of()), XContentType.JSON);
+        Source filteredMap = fromMap.filter(new SourceFilter(new String[] { "myObject" }, new String[] { "myObject.myField" }));
+        assertEquals(filteredMap.source(), Map.of("myObject", Map.of()));
+        Source fromBytes = Source.fromBytes(new BytesArray("{\"myObject\": {}}"), XContentType.JSON);
+        Source filteredBytes = fromBytes.filter(new SourceFilter(new String[] { "myObject" }, new String[] { "myObject.myField" }));
+        assertEquals(filteredBytes.source(), Map.of("myObject", Map.of()));
+    }
+
+    public void testIncludeParentAndExcludeChildSubFieldsArrays() {
+        Source fromMap = Source.fromMap(
+            Map.of("myArray", List.of(Map.<String, Object>of("myField", "myValue", "other", "otherValue"))),
+            XContentType.JSON
+        );
+        Source filteredMap = fromMap.filter(new SourceFilter(new String[] { "myArray" }, new String[] { "myArray.myField" }));
+        assertEquals(filteredMap.source(), Map.of("myArray", List.of(Map.of("other", "otherValue"))));
+        Source fromBytes = Source.fromBytes(new BytesArray("""
+            { "myArray": [ { "myField": "myValue", "other": "otherValue" } ] }"""), XContentType.JSON);
+        Source filteredBytes = fromBytes.filter(new SourceFilter(new String[] { "myArray" }, new String[] { "myArray.myField" }));
+        assertEquals(filteredBytes.source(), Map.of("myArray", List.of(Map.of("other", "otherValue"))));
+    }
+
+    public void testIncludeParentAndExcludeChildSubFieldsObjects() {
+        Source fromMap = Source.fromMap(
+            Map.of("myObject", Map.<String, Object>of("myField", "myValue", "other", "otherValue")),
+            XContentType.JSON
+        );
+        Source filteredMap = fromMap.filter(new SourceFilter(new String[] { "myObject" }, new String[] { "myObject.myField" }));
+        assertEquals(filteredMap.source(), Map.of("myObject", Map.of("other", "otherValue")));
+        Source fromBytes = Source.fromBytes(new BytesArray("""
+            { "myObject": { "myField": "myValue", "other": "otherValue" } }"""), XContentType.JSON);
+        Source filteredBytes = fromBytes.filter(new SourceFilter(new String[] { "myObject" }, new String[] { "myObject.myField" }));
+        assertEquals(filteredBytes.source(), Map.of("myObject", Map.of("other", "otherValue")));
+    }
 }