diff --git a/common/src/main/java/me/lucko/luckperms/common/storage/implementation/mongodb/MongoStorage.java b/common/src/main/java/me/lucko/luckperms/common/storage/implementation/mongodb/MongoStorage.java
index 364b92569..b07afe06a 100644
--- a/common/src/main/java/me/lucko/luckperms/common/storage/implementation/mongodb/MongoStorage.java
+++ b/common/src/main/java/me/lucko/luckperms/common/storage/implementation/mongodb/MongoStorage.java
@@ -36,6 +36,7 @@ import com.mongodb.client.MongoCollection;
 import com.mongodb.client.MongoCursor;
 import com.mongodb.client.MongoDatabase;
 import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.Indexes;
 import com.mongodb.client.model.ReplaceOptions;
 import com.mongodb.client.model.Sorts;
 import com.mongodb.client.model.UpdateOptions;
@@ -149,6 +150,7 @@ public class MongoStorage implements StorageImplementation {
         }
         
         this.database = this.mongoClient.getDatabase(this.configuration.getDatabase());
+        ensureIndexes();
     }
 
     @Override
@@ -751,4 +753,10 @@ public class MongoStorage implements StorageImplementation {
         }
     }
 
+    private void ensureIndexes() {
+        this.database.getCollection(this.prefix + "uuid").createIndex(Indexes.ascending("name"));
+        this.database.getCollection(this.prefix + "users").createIndex(Indexes.ascending("permissions.key"));
+        this.database.getCollection(this.prefix + "groups").createIndex(Indexes.ascending("permissions.key"));
+    }
+
 }
diff --git a/common/src/test/java/me/lucko/luckperms/common/storage/MongoStorageTest.java b/common/src/test/java/me/lucko/luckperms/common/storage/MongoStorageTest.java
index cc28698da..56e0b90fe 100644
--- a/common/src/test/java/me/lucko/luckperms/common/storage/MongoStorageTest.java
+++ b/common/src/test/java/me/lucko/luckperms/common/storage/MongoStorageTest.java
@@ -25,37 +25,116 @@
 
 package me.lucko.luckperms.common.storage;
 
+import com.mongodb.MongoClient;
+import com.mongodb.ServerAddress;
+import com.mongodb.client.MongoDatabase;
 import me.lucko.luckperms.common.plugin.LuckPermsPlugin;
 import me.lucko.luckperms.common.storage.implementation.StorageImplementation;
 import me.lucko.luckperms.common.storage.implementation.mongodb.MongoStorage;
 import me.lucko.luckperms.common.storage.misc.StorageCredentials;
+import org.bson.Document;
 import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
 import org.testcontainers.containers.GenericContainer;
 import org.testcontainers.utility.DockerImageName;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
 @Tag("docker")
 public class MongoStorageTest extends AbstractStorageTest {
 
+    private static final String DATABASE = "minecraft";
+    private static final String PREFIX = "luckperms_";
     private final GenericContainer<?> container = new GenericContainer<>(DockerImageName.parse("mongo"))
             .withExposedPorts(27017);
+    private String host;
+    private int port;
 
     @Override
     protected StorageImplementation makeStorage(LuckPermsPlugin plugin) throws Exception {
         this.container.start();
-        String host = this.container.getHost();
-        Integer port = this.container.getFirstMappedPort();
+        this.host = this.container.getHost();
+        this.port = this.container.getFirstMappedPort();
 
         StorageCredentials credentials = new StorageCredentials(
-                host + ":" + port,
-                "minecraft",
+                this.host + ":" + this.port,
+                DATABASE,
                 "",
                 ""
         );
-        return new MongoStorage(plugin, credentials, "", "");
+        return new MongoStorage(plugin, credentials, PREFIX, "");
     }
 
     @Override
     protected void cleanupResources() {
         this.container.stop();
     }
+
+    @Test
+    public void testIndexesAreCreatedAndInitIsIdempotent() throws Exception {
+        this.storage.shutdown();
+        this.storage.init();
+
+        try (MongoClient client = new MongoClient(new ServerAddress(this.host, this.port))) {
+            MongoDatabase database = client.getDatabase(DATABASE);
+
+            assertIndexCreatedOnce(
+                    database,
+                    PREFIX + "uuid",
+                    "_id_",
+                    new Document("_id", 1)
+            );
+
+            assertIndexCreatedOnce(
+                    database,
+                    PREFIX + "uuid",
+                    "name_1",
+                    new Document("name", 1)
+            );
+
+            assertIndexCreatedOnce(
+                    database,
+                    PREFIX + "users",
+                    "permissions.key_1",
+                    new Document("permissions.key", 1)
+            );
+
+            assertIndexCreatedOnce(
+                    database,
+                    PREFIX + "groups",
+                    "permissions.key_1",
+                    new Document("permissions.key", 1)
+            );
+        }
+    }
+
+    private static void assertIndexCreatedOnce(
+            MongoDatabase database,
+            String collectionName,
+            String indexName,
+            Document expectedKey) {
+        List<Document> collectionIndexes = database.getCollection(collectionName).listIndexes().into(new ArrayList<>());
+        Document collectionIndex = collectionIndexes.stream()
+                .filter(index -> indexName.equals(index.getString("name")))
+                .findFirst().orElse(null);
+
+        assertNotNull(collectionIndex);
+
+        assertEquals(
+                expectedKey,
+                collectionIndex.get("key", Document.class)
+        );
+
+        // Ensure index has not been duplicated.
+        assertEquals(
+                1L,
+                collectionIndexes.stream()
+                        .filter(index -> indexName.equals(index.getString("name")))
+                        .count()
+        );
+    }
 }