diff --git a/x-pack/packages/ml/aiops_log_pattern_analysis/schema.ts b/x-pack/packages/ml/aiops_log_pattern_analysis/schema.ts
index 72b1dbca38032..05254e72a651c 100644
--- a/x-pack/packages/ml/aiops_log_pattern_analysis/schema.ts
+++ b/x-pack/packages/ml/aiops_log_pattern_analysis/schema.ts
@@ -38,7 +38,6 @@ export const indicesOptionsSchema = schema.object({
   ),
   ignore_unavailable: schema.maybe(schema.boolean()),
   allow_no_indices: schema.maybe(schema.boolean()),
-  ignore_throttled: schema.maybe(schema.boolean()),
 });
 
 /**
diff --git a/x-pack/packages/ml/aiops_log_rate_analysis/api/schema_v2.ts b/x-pack/packages/ml/aiops_log_rate_analysis/api/schema_v2.ts
index 1e132f6f00e78..95c778a118454 100644
--- a/x-pack/packages/ml/aiops_log_rate_analysis/api/schema_v2.ts
+++ b/x-pack/packages/ml/aiops_log_rate_analysis/api/schema_v2.ts
@@ -45,6 +45,7 @@ export const aiopsLogRateAnalysisBase = schema.object({
   end: schema.number(),
   searchQuery: schema.string(),
   timeFieldName: schema.string(),
+  // when v2 is removed, includeFrozen should not carry over to v3+
   includeFrozen: schema.maybe(schema.boolean()),
   grouping: schema.maybe(schema.boolean()),
   /** Analysis selection time ranges */
diff --git a/x-pack/packages/ml/aiops_log_rate_analysis/queries/__mocks__/params_match_all.ts b/x-pack/packages/ml/aiops_log_rate_analysis/queries/__mocks__/params_match_all.ts
index a81ba523caa43..36d63c883ecd8 100644
--- a/x-pack/packages/ml/aiops_log_rate_analysis/queries/__mocks__/params_match_all.ts
+++ b/x-pack/packages/ml/aiops_log_rate_analysis/queries/__mocks__/params_match_all.ts
@@ -14,6 +14,5 @@ export const paramsMock = {
   baselineMax: 20,
   deviationMin: 30,
   deviationMax: 40,
-  includeFrozen: false,
   searchQuery: '{ "match_all": {} }',
 };
diff --git a/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.test.ts b/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.test.ts
deleted file mode 100644
index 33797e219fd37..0000000000000
--- a/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.test.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
- * or more contributor license agreements. Licensed under the Elastic License
- * 2.0; you may not use this file except in compliance with the Elastic License
- * 2.0.
- */
-
-import { paramsMock } from './__mocks__/params_match_all';
-
-import { getRequestBase } from './get_request_base';
-
-describe('getRequestBase', () => {
-  it('defaults to not setting `ignore_throttled`', () => {
-    const requestBase = getRequestBase(paramsMock);
-    expect(requestBase.ignore_throttled).toEqual(undefined);
-  });
-
-  it('adds `ignore_throttled=false` when `includeFrozen=true`', () => {
-    const requestBase = getRequestBase({
-      ...paramsMock,
-      includeFrozen: true,
-    });
-    expect(requestBase.ignore_throttled).toEqual(false);
-  });
-});
diff --git a/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.ts b/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.ts
index 8083cb25c12b5..8b16b5c050596 100644
--- a/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.ts
+++ b/x-pack/packages/ml/aiops_log_rate_analysis/queries/get_request_base.ts
@@ -7,8 +7,7 @@
 
 import type { AiopsLogRateAnalysisSchema } from '../api/schema';
 
-export const getRequestBase = ({ index, includeFrozen }: AiopsLogRateAnalysisSchema) => ({
+export const getRequestBase = ({ index }: AiopsLogRateAnalysisSchema) => ({
   index,
-  ...(includeFrozen ? { ignore_throttled: false } : {}),
   ignore_unavailable: true,
 });
diff --git a/x-pack/packages/ml/json_schemas/src/put___ml_anomaly_detectors__job_id__schema.json b/x-pack/packages/ml/json_schemas/src/put___ml_anomaly_detectors__job_id__schema.json
index 79a871f1ef3fa..81e1d22bdad9b 100644
--- a/x-pack/packages/ml/json_schemas/src/put___ml_anomaly_detectors__job_id__schema.json
+++ b/x-pack/packages/ml/json_schemas/src/put___ml_anomaly_detectors__job_id__schema.json
@@ -10765,10 +10765,6 @@
           "ignore_unavailable": {
             "description": "If true, missing or closed indices are not included in the response.",
             "type": "boolean"
-          },
-          "ignore_throttled": {
-            "description": "If true, concrete, expanded or aliased indices are ignored when frozen.",
-            "type": "boolean"
           }
         }
       },
@@ -10884,4 +10880,4 @@
       }
     }
   }
-}
\ No newline at end of file
+}
diff --git a/x-pack/packages/ml/json_schemas/src/put___ml_datafeeds__datafeed_id__schema.json b/x-pack/packages/ml/json_schemas/src/put___ml_datafeeds__datafeed_id__schema.json
index 575411eb3a8c2..8bf2dbfc1f529 100644
--- a/x-pack/packages/ml/json_schemas/src/put___ml_datafeeds__datafeed_id__schema.json
+++ b/x-pack/packages/ml/json_schemas/src/put___ml_datafeeds__datafeed_id__schema.json
@@ -7932,10 +7932,6 @@
           "ignore_unavailable": {
             "description": "If true, missing or closed indices are not included in the response.",
             "type": "boolean"
-          },
-          "ignore_throttled": {
-            "description": "If true, concrete, expanded or aliased indices are ignored when frozen.",
-            "type": "boolean"
           }
         }
       },
@@ -8051,4 +8047,4 @@
       }
     }
   }
-}
\ No newline at end of file
+}
diff --git a/x-pack/plugins/ml/server/models/job_service/jobs.ts b/x-pack/plugins/ml/server/models/job_service/jobs.ts
index 9c4ea6b1d3307..fa779258e5f23 100644
--- a/x-pack/plugins/ml/server/models/job_service/jobs.ts
+++ b/x-pack/plugins/ml/server/models/job_service/jobs.ts
@@ -354,6 +354,10 @@ export function jobsProvider(
     const result: { datafeed?: Datafeed; job?: Job } = { job: undefined, datafeed: undefined };
     if (datafeedResult && datafeedResult.job_id === jobId) {
       result.datafeed = datafeedResult;
+      if (result.datafeed.indices_options?.ignore_throttled !== undefined) {
+        // ignore_throttled is a deprecated setting, remove it from the response
+        delete result.datafeed.indices_options.ignore_throttled;
+      }
     }
 
     if (jobResults?.jobs?.length > 0) {
diff --git a/x-pack/plugins/ml/server/routes/schemas/datafeeds_schema.ts b/x-pack/plugins/ml/server/routes/schemas/datafeeds_schema.ts
index 27e1b6afe3364..2c61dca8859b2 100644
--- a/x-pack/plugins/ml/server/routes/schemas/datafeeds_schema.ts
+++ b/x-pack/plugins/ml/server/routes/schemas/datafeeds_schema.ts
@@ -27,7 +27,10 @@ export const indicesOptionsSchema = schema.object({
   ),
   ignore_unavailable: schema.maybe(schema.boolean()),
   allow_no_indices: schema.maybe(schema.boolean()),
+  // retaining the deprecated ignore_throttled in case an older jobs are used
+  // we don't want to fail the schema validation if this is present
   ignore_throttled: schema.maybe(schema.boolean()),
+  failure_store: schema.maybe(schema.string()),
 });
 
 export const datafeedConfigSchema = schema.object({
diff --git a/x-pack/test/functional/apps/ml/anomaly_detection_result_views/aggregated_scripted_job.ts b/x-pack/test/functional/apps/ml/anomaly_detection_result_views/aggregated_scripted_job.ts
index d2171544aa993..0d27f9afe153b 100644
--- a/x-pack/test/functional/apps/ml/anomaly_detection_result_views/aggregated_scripted_job.ts
+++ b/x-pack/test/functional/apps/ml/anomaly_detection_result_views/aggregated_scripted_job.ts
@@ -59,7 +59,6 @@ export default function ({ getService }: FtrProviderContext) {
           expand_wildcards: ['open'],
           ignore_unavailable: false,
           allow_no_indices: true,
-          ignore_throttled: true,
         },
         query: {
           match_all: {},
@@ -140,7 +139,6 @@ export default function ({ getService }: FtrProviderContext) {
           expand_wildcards: ['open'],
           ignore_unavailable: false,
           allow_no_indices: true,
-          ignore_throttled: true,
         },
         query: {
           bool: {
@@ -217,7 +215,6 @@ export default function ({ getService }: FtrProviderContext) {
           expand_wildcards: ['open'],
           ignore_unavailable: false,
           allow_no_indices: true,
-          ignore_throttled: true,
         },
         query: {
           match_all: {},
@@ -317,7 +314,6 @@ export default function ({ getService }: FtrProviderContext) {
           expand_wildcards: ['open'],
           ignore_unavailable: false,
           allow_no_indices: true,
-          ignore_throttled: true,
         },
         query: {
           bool: {