diff --git a/packages/kbn-apm-config-loader/src/config.test.ts b/packages/kbn-apm-config-loader/src/config.test.ts
index e955b175de129..01f83d43f160d 100644
--- a/packages/kbn-apm-config-loader/src/config.test.ts
+++ b/packages/kbn-apm-config-loader/src/config.test.ts
@@ -146,6 +146,35 @@ describe('ApmConfiguration', () => {
     );
   });
 
+  it('flattens the `globalLabels` object', () => {
+    const kibanaConfig = {
+      elastic: {
+        apm: {
+          globalLabels: {
+            keyOne: 'k1',
+            objectOne: {
+              objectOneKeyOne: 'o1k1',
+              objectOneKeyTwo: {
+                objectOneKeyTwoSubkeyOne: 'o1k2s1',
+              },
+            },
+          },
+        },
+      },
+    };
+    const config = new ApmConfiguration(mockedRootDir, kibanaConfig, true);
+    expect(config.getConfig('serviceName')).toEqual(
+      expect.objectContaining({
+        globalLabels: {
+          git_rev: 'sha',
+          keyOne: 'k1',
+          'objectOne.objectOneKeyOne': 'o1k1',
+          'objectOne.objectOneKeyTwo.objectOneKeyTwoSubkeyOne': 'o1k2s1',
+        },
+      })
+    );
+  });
+
   describe('env vars', () => {
     beforeEach(() => {
       delete process.env.ELASTIC_APM_ENVIRONMENT;
diff --git a/packages/kbn-apm-config-loader/src/config.ts b/packages/kbn-apm-config-loader/src/config.ts
index 8771eb042dc75..ef5f41bb8398e 100644
--- a/packages/kbn-apm-config-loader/src/config.ts
+++ b/packages/kbn-apm-config-loader/src/config.ts
@@ -13,6 +13,7 @@ import { getDataPath } from '@kbn/utils';
 import { readFileSync } from 'fs';
 import type { AgentConfigOptions } from 'elastic-apm-node';
 import type { AgentConfigOptions as RUMAgentConfigOptions } from '@elastic/apm-rum';
+import { getFlattenedObject } from '@kbn/std';
 import type { ApmConfigSchema } from './apm_config';
 
 // https://www.elastic.co/guide/en/apm/agent/nodejs/current/configuration.html
@@ -129,6 +130,15 @@ export class ApmConfiguration {
       ) {
         this.baseConfig = merge(this.baseConfig, centralizedConfig);
       }
+
+      if (this.baseConfig?.globalLabels) {
+        // Global Labels need to be a key/value pair...
+        // Dotted names will be renamed to underscored ones by the agent, but we need to provide key/value pairs
+        // https://github.com/elastic/apm-agent-nodejs/issues/4096#issuecomment-2181621221
+        this.baseConfig.globalLabels = getFlattenedObject(
+          this.baseConfig.globalLabels as Record<string, unknown>
+        );
+      }
     }
 
     return this.baseConfig;