diff --git a/src/legacy/server/config/__tests__/deprecation_warnings.js b/src/legacy/server/config/__tests__/deprecation_warnings.js
index 7cf6fdcd85ad50..3cebc730e66ded 100644
--- a/src/legacy/server/config/__tests__/deprecation_warnings.js
+++ b/src/legacy/server/config/__tests__/deprecation_warnings.js
@@ -25,7 +25,8 @@ const RUN_KBN_SERVER_STARTUP = require.resolve('./fixtures/run_kbn_server_startu
 const SETUP_NODE_ENV = require.resolve('../../../../setup_node_env');
 const SECOND = 1000;
 
-describe('config/deprecation warnings', function () {
+// FLAKY: https://github.com/elastic/kibana/issues/51479
+describe.skip('config/deprecation warnings', function () {
   this.timeout(15 * SECOND);
 
   let stdio = '';