diff --git a/spec/DefinedSchemas.spec.js b/spec/DefinedSchemas.spec.js
index e3d6fd51fe..b2cae864c1 100644
--- a/spec/DefinedSchemas.spec.js
+++ b/spec/DefinedSchemas.spec.js
@@ -371,7 +371,7 @@ describe('DefinedSchemas', () => {
       expect(schema.indexes).toEqual(indexes);
     });
 
-    it('should delete removed indexes', async () => {
+    it('should delete unknown indexes when keepUnknownIndexes is not set', async () => {
       const server = await reconfigureServer();
 
       let indexes = { complex: { createdAt: 1, updatedAt: 1 } };
@@ -393,6 +393,53 @@ describe('DefinedSchemas', () => {
       cleanUpIndexes(schema);
       expect(schema.indexes).toBeUndefined();
     });
+
+    it('should delete unknown indexes when keepUnknownIndexes is set to false', async () => {
+      const server = await reconfigureServer();
+
+      let indexes = { complex: { createdAt: 1, updatedAt: 1 } };
+
+      let schemas = { definitions: [{ className: 'Test', indexes }], keepUnknownIndexes: false };
+      await new DefinedSchemas(schemas, server.config).execute();
+
+      indexes = {};
+      schemas = { definitions: [{ className: 'Test', indexes }], keepUnknownIndexes: false };
+      // Change indexes
+      await new DefinedSchemas(schemas, server.config).execute();
+      let schema = await new Parse.Schema('Test').get();
+      cleanUpIndexes(schema);
+      expect(schema.indexes).toBeUndefined();
+
+      // Update
+      await new DefinedSchemas(schemas, server.config).execute();
+      schema = await new Parse.Schema('Test').get();
+      cleanUpIndexes(schema);
+      expect(schema.indexes).toBeUndefined();
+    });
+
+    it('should not delete unknown indexes when keepUnknownIndexes is set to true', async () => {
+      const server = await reconfigureServer();
+
+      const indexes = { complex: { createdAt: 1, updatedAt: 1 } };
+
+      let schemas = { definitions: [{ className: 'Test', indexes }], keepUnknownIndexes: true };
+      await new DefinedSchemas(schemas, server.config).execute();
+
+      schemas = { definitions: [{ className: 'Test', indexes: {} }], keepUnknownIndexes: true };
+
+      // Change indexes
+      await new DefinedSchemas(schemas, server.config).execute();
+      let schema = await new Parse.Schema('Test').get();
+      cleanUpIndexes(schema);
+      expect(schema.indexes).toEqual({ complex: { createdAt: 1, updatedAt: 1 } });
+
+      // Update
+      await new DefinedSchemas(schemas, server.config).execute();
+      schema = await new Parse.Schema('Test').get();
+      cleanUpIndexes(schema);
+      expect(schema.indexes).toEqual(indexes);
+    });
+
     xit('should keep protected indexes', async () => {
       const server = await reconfigureServer();
 
diff --git a/src/Options/Definitions.js b/src/Options/Definitions.js
index a23a0de3e5..ab25b1017d 100644
--- a/src/Options/Definitions.js
+++ b/src/Options/Definitions.js
@@ -28,6 +28,13 @@ module.exports.SchemaOptions = {
     action: parsers.booleanParser,
     default: false,
   },
+  keepUnknownIndexes: {
+    env: 'PARSE_SERVER_SCHEMA_KEEP_UNKNOWN_INDEXES',
+    help:
+      "(Optional) Keep indexes that are present in the database but not defined in the schema. Set this to `true` if you are adding indexes manually, so that they won't be removed when running schema migration. Default is `false`.",
+    action: parsers.booleanParser,
+    default: false,
+  },
   lockSchemas: {
     env: 'PARSE_SERVER_SCHEMA_LOCK_SCHEMAS',
     help:
diff --git a/src/Options/docs.js b/src/Options/docs.js
index bfba129bb2..0a8df6d137 100644
--- a/src/Options/docs.js
+++ b/src/Options/docs.js
@@ -4,6 +4,7 @@
  * @property {Function} beforeMigration Execute a callback before running schema migrations.
  * @property {Any} definitions Rest representation on Parse.Schema https://docs.parseplatform.org/rest/guide/#adding-a-schema
  * @property {Boolean} deleteExtraFields Is true if Parse Server should delete any fields not defined in a schema definition. This should only be used during development.
+ * @property {Boolean} keepUnknownIndexes (Optional) Keep indexes that are present in the database but not defined in the schema. Set this to `true` if you are adding indexes manually, so that they won't be removed when running schema migration. Default is `false`.
  * @property {Boolean} lockSchemas Is true if Parse Server will reject any attempts to modify the schema while the server is running.
  * @property {Boolean} recreateModifiedFields Is true if Parse Server should recreate any fields that are different between the current database schema and theschema definition. This should only be used during development.
  * @property {Boolean} strict Is true if Parse Server should exit if schema update fail.
diff --git a/src/Options/index.js b/src/Options/index.js
index b1827d808a..9f70700345 100644
--- a/src/Options/index.js
+++ b/src/Options/index.js
@@ -25,6 +25,9 @@ export interface SchemaOptions {
   /* Is true if Parse Server will reject any attempts to modify the schema while the server is running.
   :DEFAULT: false */
   lockSchemas: ?boolean;
+  /* (Optional) Keep indexes that are present in the database but not defined in the schema. Set this to `true` if you are adding indexes manually, so that they won't be removed when running schema migration. Default is `false`.
+  :DEFAULT: false */
+  keepUnknownIndexes: ?boolean;
   /* Execute a callback before running schema migrations. */
   beforeMigration: ?() => void | Promise<void>;
   /* Execute a callback after running schema migrations. */
diff --git a/src/SchemaMigrations/DefinedSchemas.js b/src/SchemaMigrations/DefinedSchemas.js
index cf2b1761f4..0a94a5e4ad 100644
--- a/src/SchemaMigrations/DefinedSchemas.js
+++ b/src/SchemaMigrations/DefinedSchemas.js
@@ -349,7 +349,10 @@ export class DefinedSchemas {
       Object.keys(cloudSchema.indexes).forEach(indexName => {
         if (!this.isProtectedIndex(localSchema.className, indexName)) {
           if (!localSchema.indexes || !localSchema.indexes[indexName]) {
-            newLocalSchema.deleteIndex(indexName);
+            // If keepUnknownIndex is falsy, then delete all unknown indexes from the db.
+            if(!this.schemaOptions.keepUnknownIndexes){
+              newLocalSchema.deleteIndex(indexName);
+            }
           } else if (
             !this.paramsAreEquals(localSchema.indexes[indexName], cloudSchema.indexes[indexName])
           ) {
diff --git a/src/SchemaMigrations/Migrations.js b/src/SchemaMigrations/Migrations.js
index 8768911189..23499bdba7 100644
--- a/src/SchemaMigrations/Migrations.js
+++ b/src/SchemaMigrations/Migrations.js
@@ -6,6 +6,7 @@ export interface SchemaOptions {
   deleteExtraFields: ?boolean;
   recreateModifiedFields: ?boolean;
   lockSchemas: ?boolean;
+  keepUnknownIndexes: ?boolean;
   beforeMigration: ?() => void | Promise<void>;
   afterMigration: ?() => void | Promise<void>;
 }