diff --git a/.changeset/wise-bikes-fix.md b/.changeset/wise-bikes-fix.md
new file mode 100644
index 000000000000..96628546e8a3
--- /dev/null
+++ b/.changeset/wise-bikes-fix.md
@@ -0,0 +1,5 @@
+---
+'astro': patch
+---
+
+Add warning when using headers and encoding in endpoints in SSR
diff --git a/packages/astro/src/core/app/index.ts b/packages/astro/src/core/app/index.ts
index c9ec49bd3c20..c97131b43b73 100644
--- a/packages/astro/src/core/app/index.ts
+++ b/packages/astro/src/core/app/index.ts
@@ -5,14 +5,13 @@ import type {
 	RouteData,
 	SSRElement,
 } from '../../@types/astro';
-import type { LogOptions } from '../logger/core.js';
 import type { RouteInfo, SSRManifest as Manifest } from './types';
 
 import mime from 'mime';
 import { attachToResponse, getSetCookiesFromResponse } from '../cookies/index.js';
 import { call as callEndpoint } from '../endpoint/index.js';
 import { consoleLogDestination } from '../logger/console.js';
-import { error } from '../logger/core.js';
+import { error, type LogOptions } from '../logger/core.js';
 import { joinPaths, prependForwardSlash, removeTrailingForwardSlash } from '../path.js';
 import {
 	createEnvironment,
@@ -228,7 +227,7 @@ export class App {
 			status,
 		});
 
-		const result = await callEndpoint(handler, this.#env, ctx);
+		const result = await callEndpoint(handler, this.#env, ctx, this.#logging);
 
 		if (result.type === 'response') {
 			if (result.response.headers.get('X-Astro-Response') === 'Not-Found') {
diff --git a/packages/astro/src/core/build/generate.ts b/packages/astro/src/core/build/generate.ts
index 3b163611ae75..7ae4de6a1e23 100644
--- a/packages/astro/src/core/build/generate.ts
+++ b/packages/astro/src/core/build/generate.ts
@@ -386,7 +386,7 @@ async function generatePath(
 	let encoding: BufferEncoding | undefined;
 	if (pageData.route.type === 'endpoint') {
 		const endpointHandler = mod as unknown as EndpointHandler;
-		const result = await callEndpoint(endpointHandler, env, ctx);
+		const result = await callEndpoint(endpointHandler, env, ctx, logging);
 
 		if (result.type === 'response') {
 			throwIfRedirectNotAllowed(result.response, opts.settings.config);
diff --git a/packages/astro/src/core/endpoint/dev/index.ts b/packages/astro/src/core/endpoint/dev/index.ts
index 889b82345fce..515b7aa41a8e 100644
--- a/packages/astro/src/core/endpoint/dev/index.ts
+++ b/packages/astro/src/core/endpoint/dev/index.ts
@@ -1,9 +1,10 @@
 import type { EndpointHandler } from '../../../@types/astro';
+import type { LogOptions } from '../../logger/core';
 import type { SSROptions } from '../../render/dev';
 import { createRenderContext } from '../../render/index.js';
 import { call as callEndpoint } from '../index.js';
 
-export async function call(options: SSROptions) {
+export async function call(options: SSROptions, logging: LogOptions) {
 	const {
 		env,
 		preload: [, mod],
@@ -17,5 +18,5 @@ export async function call(options: SSROptions) {
 		route: options.route,
 	});
 
-	return await callEndpoint(endpointHandler, env, ctx);
+	return await callEndpoint(endpointHandler, env, ctx, logging);
 }
diff --git a/packages/astro/src/core/endpoint/index.ts b/packages/astro/src/core/endpoint/index.ts
index 533bebddd2df..fbfa8cfd40b3 100644
--- a/packages/astro/src/core/endpoint/index.ts
+++ b/packages/astro/src/core/endpoint/index.ts
@@ -5,6 +5,7 @@ import { renderEndpoint } from '../../runtime/server/index.js';
 import { ASTRO_VERSION } from '../constants.js';
 import { AstroCookies, attachToResponse } from '../cookies/index.js';
 import { AstroError, AstroErrorData } from '../errors/index.js';
+import { LogOptions, warn } from '../logger/core.js';
 import { getParamsAndProps, GetParamsAndPropsError } from '../render/core.js';
 
 const clientAddressSymbol = Symbol.for('astro.clientAddress');
@@ -71,7 +72,8 @@ function createAPIContext({
 export async function call(
 	mod: EndpointHandler,
 	env: Environment,
-	ctx: RenderContext
+	ctx: RenderContext,
+	logging: LogOptions
 ): Promise<EndpointCallResult> {
 	const paramsAndPropsResp = await getParamsAndProps({
 		mod: mod as any,
@@ -111,6 +113,24 @@ export async function call(
 		};
 	}
 
+	if (env.ssr && !mod.prerender) {
+		if (response.hasOwnProperty('headers')) {
+			warn(
+				logging,
+				'ssr',
+				'Setting headers is not supported when returning an object. Please return an instance of Response. See https://docs.astro.build/en/core-concepts/endpoints/#server-endpoints-api-routes for more information.'
+			);
+		}
+
+		if (response.encoding) {
+			warn(
+				logging,
+				'ssr',
+				'`encoding` is ignored in SSR. To return a charset other than UTF-8, please return an instance of Response. See https://docs.astro.build/en/core-concepts/endpoints/#server-endpoints-api-routes for more information.'
+			);
+		}
+	}
+
 	return {
 		type: 'simple',
 		body: response.body,
diff --git a/packages/astro/src/vite-plugin-astro-server/route.ts b/packages/astro/src/vite-plugin-astro-server/route.ts
index 85643034f995..d26fc62d70e5 100644
--- a/packages/astro/src/vite-plugin-astro-server/route.ts
+++ b/packages/astro/src/vite-plugin-astro-server/route.ts
@@ -172,7 +172,7 @@ export async function handleRoute(
 
 	// Route successfully matched! Render it.
 	if (route.type === 'endpoint') {
-		const result = await callEndpoint(options);
+		const result = await callEndpoint(options, logging);
 		if (result.type === 'response') {
 			if (result.response.headers.get('X-Astro-Response') === 'Not-Found') {
 				const fourOhFourRoute = await matchRoute('/404', env, manifest);