diff --git a/x-pack/plugin/esql/qa/server/multi-clusters/src/javaRestTest/java/org/elasticsearch/xpack/esql/ccq/RequestIndexFilteringIT.java b/x-pack/plugin/esql/qa/server/multi-clusters/src/javaRestTest/java/org/elasticsearch/xpack/esql/ccq/RequestIndexFilteringIT.java
index 2e67ad06dc0a3..ccd9ae7b48beb 100644
--- a/x-pack/plugin/esql/qa/server/multi-clusters/src/javaRestTest/java/org/elasticsearch/xpack/esql/ccq/RequestIndexFilteringIT.java
+++ b/x-pack/plugin/esql/qa/server/multi-clusters/src/javaRestTest/java/org/elasticsearch/xpack/esql/ccq/RequestIndexFilteringIT.java
@@ -39,6 +39,7 @@
 import static org.hamcrest.Matchers.greaterThanOrEqualTo;
 import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.instanceOf;
+import static org.hamcrest.Matchers.is;
 
 @ThreadLeakFilters(filters = TestClustersThreadFilter.class)
 public class RequestIndexFilteringIT extends RequestIndexFilteringTestCase {
@@ -97,6 +98,12 @@ protected String from(String... indexName) {
 
     @Override
     public Map<String, Object> runEsql(RestEsqlTestCase.RequestObjectBuilder requestObject) throws IOException {
+        return runEsql(requestObject, true);
+    }
+
+    @Override
+    public Map<String, Object> runEsql(RestEsqlTestCase.RequestObjectBuilder requestObject, boolean checkPartialResults)
+        throws IOException {
         if (requestObject.allowPartialResults() != null) {
             assumeTrue(
                 "require allow_partial_results on local cluster",
@@ -104,7 +111,7 @@ public Map<String, Object> runEsql(RestEsqlTestCase.RequestObjectBuilder request
             );
         }
         requestObject.includeCCSMetadata(true);
-        return super.runEsql(requestObject);
+        return super.runEsql(requestObject, checkPartialResults);
     }
 
     @After
@@ -160,7 +167,30 @@ public void testIndicesDontExistRemote() throws IOException {
         indexTimestampData(docsTest1, "test1", "2024-11-26", "id1");
 
         Map<String, Object> result = runEsql(
-            timestampFilter("gte", "2020-01-01").query("FROM *:foo,*:test1 METADATA _index | SORT id1 | KEEP _index, id*")
+            timestampFilter("gte", "2020-01-01").query("FROM *:foo,*:test1 METADATA _index | SORT id1 | KEEP _index, id*"),
+            false
+        );
+
+        // `foo` index doesn't exist, so the request will currently be successful, but with partial results
+        var isPartial = result.get("is_partial");
+        assertThat(isPartial, is(true));
+        assertThat(
+            result,
+            matchesMap().entry(
+                "_clusters",
+                matchesMap().entry(
+                    "details",
+                    matchesMap().entry(
+                        "remote_cluster",
+                        matchesMap().entry(
+                            "failures",
+                            matchesList().item(
+                                matchesMap().entry("reason", matchesMap().entry("reason", "no such index [foo]").extraOk()).extraOk()
+                            )
+                        ).extraOk()
+                    ).extraOk()
+                ).extraOk()
+            ).extraOk()
         );
         @SuppressWarnings("unchecked")
         var columns = (List<List<Object>>) result.get("columns");
diff --git a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/EsqlSpecTestCase.java b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/EsqlSpecTestCase.java
index 58015f3ca410a..1f00bdf18774e 100644
--- a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/EsqlSpecTestCase.java
+++ b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/EsqlSpecTestCase.java
@@ -268,9 +268,7 @@ protected final void doTest() throws Throwable {
 
         Map<String, Object> answer = runEsql(builder.query(testCase.query), testCase.assertWarnings(deduplicateExactWarnings()));
 
-        var clusters = answer.get("_clusters");
-        var reason = "unexpected partial results" + (clusters != null ? ": _clusters=" + clusters : "");
-        assertThat(reason, answer.get("is_partial"), anyOf(nullValue(), is(false)));
+        assertNotPartial(answer);
 
         var expectedColumnsWithValues = loadCsvSpecValues(testCase.expectedResults);
 
@@ -288,6 +286,14 @@ protected final void doTest() throws Throwable {
         assertResults(expectedColumnsWithValues, actualColumns, actualValues, testCase.ignoreOrder, logger);
     }
 
+    static Map<String, Object> assertNotPartial(Map<String, Object> answer) {
+        var clusters = answer.get("_clusters");
+        var reason = "unexpected partial results" + (clusters != null ? ": _clusters=" + clusters : "");
+        assertThat(reason, answer.get("is_partial"), anyOf(nullValue(), is(false)));
+
+        return answer;
+    }
+
     /**
      * Should warnings be de-duplicated before checking for exact matches. Defaults
      * to {@code false}, but in some environments we emit duplicate warnings. We'd prefer
diff --git a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RequestIndexFilteringTestCase.java b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RequestIndexFilteringTestCase.java
index 1cb2a6a526191..1ba4365ea3e92 100644
--- a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RequestIndexFilteringTestCase.java
+++ b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RequestIndexFilteringTestCase.java
@@ -249,6 +249,11 @@ public Map<String, Object> runEsql(RestEsqlTestCase.RequestObjectBuilder request
         return RestEsqlTestCase.runEsql(requestObject, new AssertWarnings.NoWarnings(), RestEsqlTestCase.Mode.SYNC);
     }
 
+    public Map<String, Object> runEsql(RestEsqlTestCase.RequestObjectBuilder requestObject, boolean checkPartialResults)
+        throws IOException {
+        return RestEsqlTestCase.runEsql(requestObject, new AssertWarnings.NoWarnings(), RestEsqlTestCase.Mode.SYNC, checkPartialResults);
+    }
+
     protected void indexTimestampData(int docs, String indexName, String date, String differentiatorFieldName) throws IOException {
         indexTimestampDataForClient(client(), docs, indexName, date, differentiatorFieldName);
     }
diff --git a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RestEsqlTestCase.java b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RestEsqlTestCase.java
index 39a7f6f25f80e..ba7d4f2c53ae7 100644
--- a/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RestEsqlTestCase.java
+++ b/x-pack/plugin/esql/qa/server/src/main/java/org/elasticsearch/xpack/esql/qa/rest/RestEsqlTestCase.java
@@ -62,6 +62,7 @@
 import static org.elasticsearch.test.MapMatcher.assertMap;
 import static org.elasticsearch.test.MapMatcher.matchesMap;
 import static org.elasticsearch.xpack.esql.EsqlTestUtils.as;
+import static org.elasticsearch.xpack.esql.qa.rest.EsqlSpecTestCase.assertNotPartial;
 import static org.elasticsearch.xpack.esql.qa.rest.RestEsqlTestCase.Mode.ASYNC;
 import static org.elasticsearch.xpack.esql.qa.rest.RestEsqlTestCase.Mode.SYNC;
 import static org.elasticsearch.xpack.esql.type.EsqlDataTypeConverter.dateTimeToString;
@@ -1242,13 +1243,21 @@ public static Map<String, Object> runEsqlAsync(RequestObjectBuilder requestObjec
         return runEsqlAsync(requestObject, randomBoolean(), new AssertWarnings.NoWarnings());
     }
 
+    public static Map<String, Object> runEsql(
+        RequestObjectBuilder requestObject,
+        AssertWarnings assertWarnings,
+        Mode mode,
+        boolean checkPartialResults
+    ) throws IOException {
+        var results = mode == ASYNC
+            ? runEsqlAsync(requestObject, randomBoolean(), assertWarnings)
+            : runEsqlSync(requestObject, assertWarnings);
+        return checkPartialResults ? assertNotPartial(results) : results;
+    }
+
     public static Map<String, Object> runEsql(RequestObjectBuilder requestObject, AssertWarnings assertWarnings, Mode mode)
         throws IOException {
-        if (mode == ASYNC) {
-            return runEsqlAsync(requestObject, randomBoolean(), assertWarnings);
-        } else {
-            return runEsqlSync(requestObject, assertWarnings);
-        }
+        return runEsql(requestObject, assertWarnings, mode, true);
     }
 
     public static Map<String, Object> runEsqlSync(RequestObjectBuilder requestObject, AssertWarnings assertWarnings) throws IOException {