diff --git a/packages/kit/src/cli.js b/packages/kit/src/cli.js
index f80e01a461b2..e09d9711a858 100644
--- a/packages/kit/src/cli.js
+++ b/packages/kit/src/cli.js
@@ -2,7 +2,7 @@ import { existsSync } from 'fs';
 import sade from 'sade';
 import colors from 'kleur';
 import * as ports from 'port-authority';
-import { load_config } from './core/load_config/index.js';
+import { load_config } from './core/config/index.js';
 import { networkInterfaces, release } from 'os';
 
 async function get_config() {
diff --git a/packages/kit/src/core/build/index.js b/packages/kit/src/core/build/index.js
index e5c6f4c2ffd6..8a1664b9331e 100644
--- a/packages/kit/src/core/build/index.js
+++ b/packages/kit/src/core/build/index.js
@@ -3,6 +3,7 @@ import path from 'path';
 import { rimraf } from '../filesystem/index.js';
 import create_manifest_data from '../../core/create_manifest_data/index.js';
 import { copy_assets, get_no_external, posixify, resolve_entry } from '../utils.js';
+import { deep_merge, print_config_conflicts } from '../config/index.js';
 import { create_app } from '../../core/create_app/index.js';
 import vite from 'vite';
 import { svelte } from '@sveltejs/vite-plugin-svelte';
@@ -134,19 +135,17 @@ async function build_client({
 	/** @type {any} */
 	const user_config = config.kit.vite();
 
-	await vite.build({
-		...user_config,
+	/** @type {[any, string[]]} */
+	const [merged_config, conflicts] = deep_merge(user_config, {
 		configFile: false,
 		root: cwd,
 		base,
 		build: {
-			...user_config.build,
 			cssCodeSplit: true,
 			manifest: true,
 			outDir: client_out_dir,
 			polyfillDynamicImport: false,
 			rollupOptions: {
-				...(user_config.build && user_config.build.rollupOptions),
 				input,
 				output: {
 					entryFileNames: '[name]-[hash].js',
@@ -157,15 +156,12 @@ async function build_client({
 			}
 		},
 		resolve: {
-			...user_config.resolve,
 			alias: {
-				...(user_config.resolve && user_config.resolve.alias),
 				$app: path.resolve(`${build_dir}/runtime/app`),
 				$lib: config.kit.files.lib
 			}
 		},
 		plugins: [
-			...(user_config.plugins || []),
 			svelte({
 				extensions: config.extensions,
 				emitCss: !config.kit.amp
@@ -173,6 +169,10 @@ async function build_client({
 		]
 	});
 
+	print_config_conflicts(conflicts, 'kit.vite.', 'build_client');
+
+	await vite.build(merged_config);
+
 	/** @type {ClientManifest} */
 	const client_manifest = JSON.parse(fs.readFileSync(client_manifest_file, 'utf-8'));
 	fs.renameSync(client_manifest_file, `${output_dir}/manifest.json`); // inspectable but not shipped
@@ -395,19 +395,17 @@ async function build_server(
 	/** @type {any} */
 	const user_config = config.kit.vite();
 
-	await vite.build({
-		...user_config,
+	/** @type {[any, string[]]} */
+	const [merged_config, conflicts] = deep_merge(user_config, {
 		configFile: false,
 		root: cwd,
 		base,
 		build: {
 			target: 'es2018',
-			...user_config.build,
 			ssr: true,
 			outDir: `${output_dir}/server`,
 			polyfillDynamicImport: false,
 			rollupOptions: {
-				...(user_config.build && user_config.build.rollupOptions),
 				input: {
 					app: app_file
 				},
@@ -422,15 +420,12 @@ async function build_server(
 			}
 		},
 		resolve: {
-			...user_config.resolve,
 			alias: {
-				...(user_config.resolve && user_config.resolve.alias),
 				$app: path.resolve(`${build_dir}/runtime/app`),
 				$lib: config.kit.files.lib
 			}
 		},
 		plugins: [
-			...(user_config.plugins || []),
 			svelte({
 				extensions: config.extensions
 			})
@@ -440,7 +435,6 @@ async function build_server(
 		// so we need to ignore the fact that it's missing
 		// @ts-ignore
 		ssr: {
-			...user_config.ssr,
 			// note to self: this _might_ need to be ['svelte', '@sveltejs/kit', ...get_no_external()]
 			// but I'm honestly not sure. roll with this for now and see if it's ok
 			noExternal: get_no_external(cwd, user_config.ssr && user_config.ssr.noExternal)
@@ -449,6 +443,10 @@ async function build_server(
 			entries: []
 		}
 	});
+
+	print_config_conflicts(conflicts, 'kit.vite.', 'build_server');
+
+	await vite.build(merged_config);
 }
 
 /**
@@ -504,20 +502,18 @@ async function build_service_worker(
 	/** @type {any} */
 	const user_config = config.kit.vite();
 
-	await vite.build({
-		...user_config,
+	/** @type {[any, string[]]} */
+	const [merged_config, conflicts] = deep_merge(user_config, {
 		configFile: false,
 		root: cwd,
 		base,
 		build: {
-			...user_config.build,
 			lib: {
 				entry: service_worker_entry_file,
 				name: 'app',
 				formats: ['es']
 			},
 			rollupOptions: {
-				...(user_config.build && user_config.build.rollupOptions),
 				output: {
 					entryFileNames: 'service-worker.js'
 				}
@@ -526,9 +522,7 @@ async function build_service_worker(
 			emptyOutDir: false
 		},
 		resolve: {
-			...user_config.resolve,
 			alias: {
-				...(user_config.resolve && user_config.resolve.alias),
 				'$service-worker': path.resolve(`${build_dir}/runtime/service-worker`)
 			}
 		},
@@ -536,6 +530,10 @@ async function build_service_worker(
 			entries: []
 		}
 	});
+
+	print_config_conflicts(conflicts, 'kit.vite.', 'build_service_worker');
+
+	await vite.build(merged_config);
 }
 
 /** @param {string[]} array */
diff --git a/packages/kit/src/core/load_config/index.js b/packages/kit/src/core/config/index.js
similarity index 63%
rename from packages/kit/src/core/load_config/index.js
rename to packages/kit/src/core/config/index.js
index 7973a6fc8a3f..f3a0ab0f6f91 100644
--- a/packages/kit/src/core/load_config/index.js
+++ b/packages/kit/src/core/config/index.js
@@ -2,6 +2,7 @@ import options from './options.js';
 import * as url from 'url';
 import path from 'path';
 import fs from 'fs';
+import { logger } from '../utils.js';
 
 /** @typedef {import('./types').ConfigDefinition} ConfigDefinition */
 
@@ -145,3 +146,76 @@ export function validate_config(config) {
 
 	return validated;
 }
+
+/**
+ * Merges b into a, recursively, mutating a.
+ * @param {Record<string, any>} a
+ * @param {Record<string, any>} b
+ * @param {string[]} conflicts array to accumulate conflicts in
+ * @param {string[]} path array of property names representing the current
+ *     location in the tree
+ */
+function merge_into(a, b, conflicts = [], path = []) {
+	/**
+	 * @param {any} x
+	 */
+	const is_object = (x) => typeof x === 'object' && !Array.isArray(x);
+
+	for (const prop in b) {
+		if (is_object(b[prop])) {
+			if (!is_object(a[prop])) {
+				if (a[prop] !== undefined) {
+					conflicts.push([...path, prop].join('.'));
+				}
+				a[prop] = {};
+			}
+			merge_into(a[prop], b[prop], conflicts, [...path, prop]);
+		} else if (Array.isArray(b[prop])) {
+			if (!Array.isArray(a[prop])) {
+				if (a[prop] !== undefined) {
+					conflicts.push([...path, prop].join('.'));
+				}
+				a[prop] = [];
+			}
+			a[prop].push(...b[prop]);
+		} else {
+			if (a[prop] !== undefined) {
+				conflicts.push([...path, prop].join('.'));
+			}
+			a[prop] = b[prop];
+		}
+	}
+}
+
+/**
+ * Takes zero or more objects and returns a new object that has all the values
+ * deeply merged together. None of the original objects will be mutated at any
+ * level, and the returned object will have no references to the original
+ * objects at any depth. If there's a conflict the last one wins, except for
+ * arrays which will be combined.
+ * @param {...Object} objects
+ * @returns {[Record<string, any>, string[]]} a 2-tuple with the merged object,
+ *     and a list of merge conflicts if there were any, in dotted notation
+ */
+export function deep_merge(...objects) {
+	const result = {};
+	/** @type {string[]} */
+	const conflicts = [];
+	objects.forEach((o) => merge_into(result, o, conflicts));
+	return [result, conflicts];
+}
+
+/**
+ * @param {string[]} conflicts - array of conflicts in dotted notation
+ * @param {string=} pathPrefix - prepended in front of the path
+ * @param {string=} scope - used to prefix the whole error message
+ */
+export function print_config_conflicts(conflicts, pathPrefix = '', scope) {
+	const prefix = scope ? scope + ': ' : '';
+	const log = logger({ verbose: false });
+	conflicts.forEach((conflict) => {
+		log.error(
+			`${prefix}The value for ${pathPrefix}${conflict} specified in svelte.config.js has been ignored. This option is controlled by SvelteKit.`
+		);
+	});
+}
diff --git a/packages/kit/src/core/load_config/index.spec.js b/packages/kit/src/core/config/index.spec.js
similarity index 66%
rename from packages/kit/src/core/load_config/index.spec.js
rename to packages/kit/src/core/config/index.spec.js
index 6f11b28d79c3..bd53d4f6e6b2 100644
--- a/packages/kit/src/core/load_config/index.spec.js
+++ b/packages/kit/src/core/config/index.spec.js
@@ -1,6 +1,6 @@
-import { test } from 'uvu';
+import { test, suite } from 'uvu';
 import * as assert from 'uvu/assert';
-import { validate_config } from './index.js';
+import { validate_config, deep_merge } from './index.js';
 
 test('fills in defaults', () => {
 	const validated = validate_config({});
@@ -298,3 +298,152 @@ validate_paths(
 );
 
 test.run();
+
+const deepMergeSuite = suite('deep_merge');
+
+deepMergeSuite('basic test no conflicts', async () => {
+	const [merged, conflicts] = deep_merge(
+		{
+			version: 1,
+			animalSounds: {
+				cow: 'moo'
+			}
+		},
+		{
+			animalSounds: {
+				duck: 'quack'
+			},
+			locale: 'en_US'
+		}
+	);
+	assert.equal(merged, {
+		version: 1,
+		locale: 'en_US',
+		animalSounds: {
+			cow: 'moo',
+			duck: 'quack'
+		}
+	});
+	assert.equal(conflicts, []);
+});
+
+deepMergeSuite('three way merge no conflicts', async () => {
+	const [merged, conflicts] = deep_merge(
+		{
+			animalSounds: {
+				cow: 'moo'
+			}
+		},
+		{
+			animalSounds: {
+				duck: 'quack'
+			}
+		},
+		{
+			animalSounds: {
+				dog: {
+					singular: 'bark',
+					plural: 'barks'
+				}
+			}
+		}
+	);
+	assert.equal(merged, {
+		animalSounds: {
+			cow: 'moo',
+			duck: 'quack',
+			dog: {
+				singular: 'bark',
+				plural: 'barks'
+			}
+		}
+	});
+	assert.equal(conflicts, []);
+});
+
+deepMergeSuite('merge with conflicts', async () => {
+	const [merged, conflicts] = deep_merge(
+		{
+			person: {
+				firstName: 'John',
+				lastName: 'Doe',
+				address: {
+					line1: '123 Main St',
+					city: 'Seattle',
+					state: 'WA'
+				}
+			}
+		},
+		{
+			person: {
+				middleInitial: 'Q',
+				address: '123 Main St, Seattle, WA'
+			}
+		}
+	);
+	assert.equal(merged, {
+		person: {
+			firstName: 'John',
+			middleInitial: 'Q',
+			lastName: 'Doe',
+			address: '123 Main St, Seattle, WA'
+		}
+	});
+	assert.equal(conflicts, ['person.address']);
+});
+
+deepMergeSuite('merge with arrays', async () => {
+	const [merged] = deep_merge(
+		{
+			paths: ['/foo', '/bar']
+		},
+		{
+			paths: ['/alpha', '/beta']
+		}
+	);
+	assert.equal(merged, {
+		paths: ['/foo', '/bar', '/alpha', '/beta']
+	});
+});
+
+deepMergeSuite('empty', async () => {
+	const [merged] = deep_merge();
+	assert.equal(merged, {});
+});
+
+deepMergeSuite('mutability safety', () => {
+	const input1 = {
+		person: {
+			firstName: 'John',
+			lastName: 'Doe',
+			address: {
+				line1: '123 Main St',
+				city: 'Seattle'
+			}
+		}
+	};
+	const input2 = {
+		person: {
+			middleInitial: 'L',
+			lastName: 'Smith',
+			address: {
+				state: 'WA'
+			}
+		}
+	};
+	const snapshot1 = JSON.stringify(input1);
+	const snapshot2 = JSON.stringify(input2);
+
+	const [merged] = deep_merge(input1, input2);
+
+	// Mess with the result
+	merged.person.middleInitial = 'Z';
+	merged.person.address.zipCode = '98103';
+	merged.person = {};
+
+	// Make sure nothing in the inputs changed
+	assert.snapshot(snapshot1, JSON.stringify(input1));
+	assert.snapshot(snapshot2, JSON.stringify(input2));
+});
+
+deepMergeSuite.run();
diff --git a/packages/kit/src/core/load_config/options.js b/packages/kit/src/core/config/options.js
similarity index 100%
rename from packages/kit/src/core/load_config/options.js
rename to packages/kit/src/core/config/options.js
diff --git a/packages/kit/src/core/load_config/test/fixtures/default-cjs/src/app.html b/packages/kit/src/core/config/test/fixtures/default-cjs/src/app.html
similarity index 100%
rename from packages/kit/src/core/load_config/test/fixtures/default-cjs/src/app.html
rename to packages/kit/src/core/config/test/fixtures/default-cjs/src/app.html
diff --git a/packages/kit/src/core/load_config/test/fixtures/default-cjs/svelte.config.cjs b/packages/kit/src/core/config/test/fixtures/default-cjs/svelte.config.cjs
similarity index 100%
rename from packages/kit/src/core/load_config/test/fixtures/default-cjs/svelte.config.cjs
rename to packages/kit/src/core/config/test/fixtures/default-cjs/svelte.config.cjs
diff --git a/packages/kit/src/core/load_config/test/fixtures/default-esm/src/app.html b/packages/kit/src/core/config/test/fixtures/default-esm/src/app.html
similarity index 100%
rename from packages/kit/src/core/load_config/test/fixtures/default-esm/src/app.html
rename to packages/kit/src/core/config/test/fixtures/default-esm/src/app.html
diff --git a/packages/kit/src/core/load_config/test/fixtures/default-esm/svelte.config.js b/packages/kit/src/core/config/test/fixtures/default-esm/svelte.config.js
similarity index 100%
rename from packages/kit/src/core/load_config/test/fixtures/default-esm/svelte.config.js
rename to packages/kit/src/core/config/test/fixtures/default-esm/svelte.config.js
diff --git a/packages/kit/src/core/load_config/test/index.js b/packages/kit/src/core/config/test/index.js
similarity index 100%
rename from packages/kit/src/core/load_config/test/index.js
rename to packages/kit/src/core/config/test/index.js
diff --git a/packages/kit/src/core/load_config/types.d.ts b/packages/kit/src/core/config/types.d.ts
similarity index 100%
rename from packages/kit/src/core/load_config/types.d.ts
rename to packages/kit/src/core/config/types.d.ts
diff --git a/packages/kit/src/core/dev/index.js b/packages/kit/src/core/dev/index.js
index 7c1dc4953777..7bbb20e7454a 100644
--- a/packages/kit/src/core/dev/index.js
+++ b/packages/kit/src/core/dev/index.js
@@ -12,6 +12,7 @@ import { rimraf } from '../filesystem/index.js';
 import { respond } from '../../runtime/server/index.js';
 import { getRawBody } from '../node/index.js';
 import { copy_assets, get_no_external, resolve_entry } from '../utils.js';
+import { deep_merge, print_config_conflicts } from '../config/index.js';
 import { svelte } from '@sveltejs/vite-plugin-svelte';
 import { get_server } from '../server/index.js';
 import '../../install-fetch.js';
@@ -86,18 +87,13 @@ class Watcher extends EventEmitter {
 
 		const alias = user_config.resolve && user_config.resolve.alias;
 
-		/**
-		 * @type {vite.ViteDevServer}
-		 */
-		this.vite = await vite.createServer({
-			...user_config,
+		/** @type {[any, string[]]} */
+		const [merged_config, conflicts] = deep_merge(user_config, {
 			configFile: false,
 			root: this.cwd,
 			resolve: {
-				...user_config.resolve,
 				alias: Array.isArray(alias)
 					? [
-							...alias,
 							{
 								find: '$app',
 								replacement: path.resolve(`${this.dir}/runtime/app`)
@@ -108,13 +104,11 @@ class Watcher extends EventEmitter {
 							}
 					  ]
 					: {
-							...alias,
 							$app: path.resolve(`${this.dir}/runtime/app`),
 							$lib: this.config.kit.files.lib
 					  }
 			},
 			plugins: [
-				...(user_config.plugins || []),
 				svelte({
 					extensions: this.config.extensions,
 					emitCss: !this.config.kit.amp
@@ -122,23 +116,26 @@ class Watcher extends EventEmitter {
 			],
 			publicDir: this.config.kit.files.assets,
 			server: {
-				...user_config.server,
 				middlewareMode: true,
 				hmr: {
-					...(user_config.server && user_config.server.hmr),
 					...(this.https ? { server: this.server, port: this.port } : {})
 				}
 			},
 			optimizeDeps: {
-				...user_config.optimizeDeps,
 				entries: []
 			},
 			ssr: {
-				...user_config.ssr,
 				noExternal: get_no_external(this.cwd, user_config.ssr && user_config.ssr.noExternal)
 			}
 		});
 
+		print_config_conflicts(conflicts, 'kit.vite.');
+
+		/**
+		 * @type {vite.ViteDevServer}
+		 */
+		this.vite = await vite.createServer(merged_config);
+
 		const validator = this.config.kit.amp && (await amp_validator.getInstance());
 
 		/**
diff --git a/packages/kit/test/test.js b/packages/kit/test/test.js
index 78c4a3ae62d8..b70cd5876d2e 100644
--- a/packages/kit/test/test.js
+++ b/packages/kit/test/test.js
@@ -6,7 +6,7 @@ import { chromium } from 'playwright-chromium';
 import { dev } from '../src/core/dev/index.js';
 import { build } from '../src/core/build/index.js';
 import { start } from '../src/core/start/index.js';
-import { load_config } from '../src/core/load_config/index.js';
+import { load_config } from '../src/core/config/index.js';
 import { fileURLToPath, pathToFileURL } from 'url';
 import { format } from 'util';