diff --git a/java/google/registry/tools/server/KillAllDomainApplicationsAction.java b/java/google/registry/tools/server/KillAllDomainApplicationsAction.java
index 8b639ba09..0c9673b20 100644
--- a/java/google/registry/tools/server/KillAllDomainApplicationsAction.java
+++ b/java/google/registry/tools/server/KillAllDomainApplicationsAction.java
@@ -75,20 +75,34 @@ public class KillAllDomainApplicationsAction implements Runnable {
                   getContext().incrementCounter("applications already deleted");
                   return;
                 }
+
                 Key<DomainApplication> applicationKey = Key.create(application);
                 DomainApplicationIndex dai =
                     ofy().load().key(DomainApplicationIndex.createKey(application)).now();
                 EppResourceIndex eri =
                     ofy().load().entity(EppResourceIndex.create(applicationKey)).now();
-                if (dai == null || eri == null) {
+
+                if (dai == null) {
                   logger.atSevere().log(
-                      "Missing index(es) for application %s; skipping.", applicationKey);
-                  getContext().incrementCounter("missing indexes");
-                  return;
+                      "Missing domain application index for application %s.", applicationKey);
+                  getContext().incrementCounter("missing domain application indexes");
+                } else {
+                  ofy().delete().entity(dai);
                 }
+
+                // This case shouldn't be possible except in extremely rare circumstances, as this
+                // mapreduce itself is relying on EPP resource indexes to load the domain
+                // applications to delete.
+                if (eri == null) {
+                  logger.atSevere().log(
+                      "Missing EPP resource index for application %s.", applicationKey);
+                  getContext().incrementCounter("missing EPP resource indexes");
+                } else {
+                  ofy().delete().entity(eri);
+                }
+
                 // Delete the application, its descendents, and the indexes.
                 ofy().delete().keys(ofy().load().ancestor(application).keys());
-                ofy().delete().entities(dai, eri);
                 logger.atInfo().log("Deleted domain application %s.", applicationKey);
                 getContext().incrementCounter("applications deleted");
               });
diff --git a/javatests/google/registry/tools/server/KillAllDomainApplicationsActionTest.java b/javatests/google/registry/tools/server/KillAllDomainApplicationsActionTest.java
index 102df8adf..544457a0f 100644
--- a/javatests/google/registry/tools/server/KillAllDomainApplicationsActionTest.java
+++ b/javatests/google/registry/tools/server/KillAllDomainApplicationsActionTest.java
@@ -16,6 +16,7 @@ package google.registry.tools.server;
 
 import static com.google.common.truth.Truth.assertThat;
 import static google.registry.model.ofy.ObjectifyService.ofy;
+import static google.registry.testing.DatastoreHelper.createTld;
 import static google.registry.testing.DatastoreHelper.createTlds;
 import static google.registry.testing.DatastoreHelper.persistActiveContact;
 import static google.registry.testing.DatastoreHelper.persistActiveDomain;
@@ -91,4 +92,26 @@ public class KillAllDomainApplicationsActionTest
                 .entities(application, applicationEri, applicationDai, applicationHistoryEntry))
         .isEmpty();
   }
+
+  @Test
+  public void test_deletesApplication_evenWhenIndexIsMissing() throws Exception {
+    createTld("tld1");
+    DomainApplication application = persistActiveDomainApplication("applied.tld1");
+    EppResourceIndex applicationEri =
+        ofy().load().entity(EppResourceIndex.create(Key.create(application))).now();
+    HistoryEntry applicationHistoryEntry =
+        persistResource(new HistoryEntry.Builder().setParent(application).build());
+
+    // Delete the domain application index.
+    ofy().transact(() -> ofy().delete().key(DomainApplicationIndex.createKey(application)).now());
+    ofy().clearSessionCache();
+
+    runMapreduce();
+    ofy().clearSessionCache();
+
+    // Check that the domain application and history entry were deleted even though the indexes
+    // couldn't be found.
+    assertThat(ofy().load().entities(application, applicationEri, applicationHistoryEntry))
+        .isEmpty();
+  }
 }