diff --git a/src/core/server/config/object_to_config_adapter.test.ts b/src/core/server/config/object_to_config_adapter.test.ts
new file mode 100644
index 0000000000000..af41741e6208a
--- /dev/null
+++ b/src/core/server/config/object_to_config_adapter.test.ts
@@ -0,0 +1,53 @@
+/*
+ * Licensed to Elasticsearch B.V. under one or more contributor
+ * license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright
+ * ownership. Elasticsearch B.V. licenses this file to you under
+ * the Apache License, Version 2.0 (the "License"); you may
+ * not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import { ObjectToConfigAdapter } from './object_to_config_adapter';
+
+describe('ObjectToConfigAdapter', () => {
+  describe('#getFlattenedPaths()', () => {
+    it('considers arrays as final values', () => {
+      const data = {
+        string: 'string',
+        array: ['an', 'array'],
+      };
+      const config = new ObjectToConfigAdapter(data);
+
+      expect(config.getFlattenedPaths()).toEqual(['string', 'array']);
+    });
+
+    it('handles nested arrays', () => {
+      const data = {
+        string: 'string',
+        array: ['an', 'array'],
+        nested: {
+          number: 12,
+          array: [{ key: 1 }, { key: 2 }],
+        },
+      };
+      const config = new ObjectToConfigAdapter(data);
+
+      expect(config.getFlattenedPaths()).toEqual([
+        'string',
+        'array',
+        'nested.number',
+        'nested.array',
+      ]);
+    });
+  });
+});
diff --git a/src/core/server/config/object_to_config_adapter.ts b/src/core/server/config/object_to_config_adapter.ts
index b6ec772603565..d4c2f73364060 100644
--- a/src/core/server/config/object_to_config_adapter.ts
+++ b/src/core/server/config/object_to_config_adapter.ts
@@ -19,6 +19,7 @@
 
 import { cloneDeep, get, has, set } from 'lodash';
 
+import { getFlattenedObject } from '../../utils';
 import { Config, ConfigPath } from './';
 
 /**
@@ -41,24 +42,10 @@ export class ObjectToConfigAdapter implements Config {
   }
 
   public getFlattenedPaths() {
-    return [...flattenObjectKeys(this.rawConfig)];
+    return Object.keys(getFlattenedObject(this.rawConfig));
   }
 
   public toRaw() {
     return cloneDeep(this.rawConfig);
   }
 }
-
-function* flattenObjectKeys(
-  obj: { [key: string]: any },
-  path: string = ''
-): IterableIterator<string> {
-  if (typeof obj !== 'object' || obj === null) {
-    yield path;
-  } else {
-    for (const [key, value] of Object.entries(obj)) {
-      const newPath = path !== '' ? `${path}.${key}` : key;
-      yield* flattenObjectKeys(value, newPath);
-    }
-  }
-}
diff --git a/src/core/server/legacy/config/get_unused_config_keys.test.ts b/src/core/server/legacy/config/get_unused_config_keys.test.ts
index c4452fc6a1209..2106a0748d814 100644
--- a/src/core/server/legacy/config/get_unused_config_keys.test.ts
+++ b/src/core/server/legacy/config/get_unused_config_keys.test.ts
@@ -200,6 +200,24 @@ describe('getUnusedConfigKeys', () => {
     ).toEqual(['foo.dolly']);
   });
 
+  it('handles array values', async () => {
+    expect(
+      await getUnusedConfigKeys({
+        coreHandledConfigPaths: ['core', 'array'],
+        pluginSpecs: [],
+        disabledPluginSpecs: [],
+        settings: {
+          core: {
+            prop: 'value',
+            array: [1, 2, 3],
+          },
+          array: ['some', 'values'],
+        },
+        legacyConfig: getConfig({}),
+      })
+    ).toEqual([]);
+  });
+
   describe('using deprecation', () => {
     it('should use the plugin deprecations provider', async () => {
       expect(
diff --git a/src/core/utils/get_flattened_object.test.ts b/src/core/utils/get_flattened_object.test.ts
new file mode 100644
index 0000000000000..26a4c5f1eb1fa
--- /dev/null
+++ b/src/core/utils/get_flattened_object.test.ts
@@ -0,0 +1,46 @@
+/*
+ * Licensed to Elasticsearch B.V. under one or more contributor
+ * license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright
+ * ownership. Elasticsearch B.V. licenses this file to you under
+ * the Apache License, Version 2.0 (the "License"); you may
+ * not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import { getFlattenedObject } from './get_flattened_object';
+
+describe('getFlattenedObject()', () => {
+  it('throws when rootValue is not an object or is an array', () => {
+    expect(() => getFlattenedObject(1 as any)).toThrowError();
+    expect(() => getFlattenedObject(Infinity as any)).toThrowError();
+    expect(() => getFlattenedObject(NaN as any)).toThrowError();
+    expect(() => getFlattenedObject(false as any)).toThrowError();
+    expect(() => getFlattenedObject(null as any)).toThrowError();
+    expect(() => getFlattenedObject(undefined as any)).toThrowError();
+    expect(() => getFlattenedObject([])).toThrowError();
+  });
+
+  it('flattens objects', () => {
+    expect(getFlattenedObject({ a: 'b' })).toEqual({ a: 'b' });
+    expect(getFlattenedObject({ a: { b: 'c' } })).toEqual({ 'a.b': 'c' });
+    expect(getFlattenedObject({ a: { b: 'c' }, d: { e: 'f' } })).toEqual({
+      'a.b': 'c',
+      'd.e': 'f',
+    });
+  });
+
+  it('does not flatten arrays', () => {
+    expect(getFlattenedObject({ a: ['b'] })).toEqual({ a: ['b'] });
+    expect(getFlattenedObject({ a: { b: ['c', 'd'] } })).toEqual({ 'a.b': ['c', 'd'] });
+  });
+});
diff --git a/src/core/utils/get_flattened_object.ts b/src/core/utils/get_flattened_object.ts
new file mode 100644
index 0000000000000..ce03793284236
--- /dev/null
+++ b/src/core/utils/get_flattened_object.ts
@@ -0,0 +1,53 @@
+/*
+ * Licensed to Elasticsearch B.V. under one or more contributor
+ * license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright
+ * ownership. Elasticsearch B.V. licenses this file to you under
+ * the Apache License, Version 2.0 (the "License"); you may
+ * not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+function shouldReadKeys(value: unknown): value is Record<string, any> {
+  return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+
+/**
+ *  Flattens a deeply nested object to a map of dot-separated
+ *  paths pointing to all primitive values **and arrays**
+ *  from `rootValue`.
+ *
+ *  example:
+ *    getFlattenedObject({ a: { b: 1, c: [2,3] } })
+ *    // => { 'a.b': 1, 'a.c': [2,3] }
+ *
+ *  @param {Object} rootValue
+ *  @returns {Object}
+ */
+export function getFlattenedObject(rootValue: Record<string, any>) {
+  if (!shouldReadKeys(rootValue)) {
+    throw new TypeError(`Root value is not flatten-able, received ${rootValue}`);
+  }
+
+  const result: { [key: string]: any } = {};
+  (function flatten(prefix, object) {
+    for (const [key, value] of Object.entries(object)) {
+      const path = prefix ? `${prefix}.${key}` : key;
+      if (shouldReadKeys(value)) {
+        flatten(path, value);
+      } else {
+        result[path] = value;
+      }
+    }
+  })('', rootValue);
+  return result;
+}
diff --git a/src/core/utils/index.ts b/src/core/utils/index.ts
index 7c8ed481c0a7d..2bb44e987d676 100644
--- a/src/core/utils/index.ts
+++ b/src/core/utils/index.ts
@@ -28,3 +28,4 @@ export * from './pick';
 export * from './promise';
 export * from './url';
 export * from './unset';
+export * from './get_flattened_object';