diff --git a/.changeset/merge-headers-fix.md b/.changeset/merge-headers-fix.md
new file mode 100644
index 00000000..2a4ee108
--- /dev/null
+++ b/.changeset/merge-headers-fix.md
@@ -0,0 +1,5 @@
+---
+"@mcansh/remix-fastify": patch
+---
+
+Merge headers set by Fastify with headers from Remix instead of overriding them. This fixes an issue where headers like `Link` set by Fastify before calling the Remix handler were being overridden by headers from the Remix response.
diff --git a/packages/remix-fastify/__tests__/server.test.ts b/packages/remix-fastify/__tests__/server.test.ts
index 7de7c9e7..e499d8b2 100644
--- a/packages/remix-fastify/__tests__/server.test.ts
+++ b/packages/remix-fastify/__tests__/server.test.ts
@@ -206,6 +206,42 @@ function runTests(
           "third=three; Expires=Wed, 21 Oct 2015 07:28:00 GMT; Path=/; HttpOnly; Secure; SameSite=Lax",
         ]);
       });
+
+      it(`[${name}] merges headers set by Fastify with headers from Remix`, async () => {
+        mockedHandler.mockImplementation(() => async () => {
+          let headers = new Headers();
+          headers.append("Link", "</remix-resource.css>; rel=preload; as=style");
+          headers.append("Link", "</remix-script.js>; rel=modulepreload");
+          return new Response(null, { headers });
+        });
+
+        let app = fastify();
+        app.all("*", async (request, reply) => {
+          // Simulate Fastify setting Link headers before Remix handler
+          reply.header("Link", "</fonts/my-font.woff2>; rel=preload; as=font; crossorigin");
+          
+          let handler = createRequestHandler({
+            // @ts-expect-error - We don't have a real app to test
+            build: undefined,
+          });
+          
+          return handler(request, reply);
+        });
+
+        let response = await app.inject("/");
+
+        expect(response.headers["link"]).toBeDefined();
+        
+        // Should contain both Fastify's header and Remix's headers
+        let linkHeaders = Array.isArray(response.headers["link"]) 
+          ? response.headers["link"] 
+          : [response.headers["link"]];
+        
+        expect(linkHeaders).toHaveLength(3);
+        expect(linkHeaders[0]).toBe("</fonts/my-font.woff2>; rel=preload; as=font; crossorigin");
+        expect(linkHeaders[1]).toBe("</remix-resource.css>; rel=preload; as=style");
+        expect(linkHeaders[2]).toBe("</remix-script.js>; rel=modulepreload");
+      });
     });
   });
 
diff --git a/packages/remix-fastify/src/shared.ts b/packages/remix-fastify/src/shared.ts
index 44ecbd22..99eff834 100644
--- a/packages/remix-fastify/src/shared.ts
+++ b/packages/remix-fastify/src/shared.ts
@@ -109,8 +109,42 @@ export async function sendResponse<Server extends HttpServer>(
 ): Promise<void> {
   reply.status(nodeResponse.status);
 
-  for (let [key, values] of nodeResponse.headers.entries()) {
-    reply.headers({ [key]: values });
+  // Collect all headers from the response first
+  let responseHeaders = new Map<string, string[]>();
+  for (let [key, value] of nodeResponse.headers.entries()) {
+    if (!responseHeaders.has(key)) {
+      responseHeaders.set(key, []);
+    }
+    // The Web Headers API treats Set-Cookie specially: each value appears as a separate
+    // entry when iterating. For all other headers, multiple values are combined with ", ".
+    // We split non-Set-Cookie headers on ", " to enable proper merging with existing headers.
+    // Note: This split is imperfect for headers that contain commas in their values
+    // (like some Cache-Control directives), but it's necessary because the Headers API
+    // has already combined them and provides no way to get the original separate values.
+    // The Link header (the primary use case from the issue) works correctly with this approach.
+    if (key.toLowerCase() === "set-cookie") {
+      responseHeaders.get(key)!.push(value);
+    } else {
+      let splitValues = value.split(", ");
+      responseHeaders.get(key)!.push(...splitValues);
+    }
+  }
+
+  // Now set headers, merging with any existing headers on the reply
+  for (let [key, values] of responseHeaders.entries()) {
+    let existingHeader = reply.hasHeader(key) ? reply.getHeader(key) : undefined;
+    
+    if (existingHeader !== undefined) {
+      // Header exists on reply - merge with response headers
+      let existingValues = Array.isArray(existingHeader) 
+        ? existingHeader 
+        : [String(existingHeader)];
+      let mergedValues = [...existingValues, ...values];
+      reply.header(key, mergedValues);
+    } else {
+      // No existing header on reply - just set response headers
+      reply.header(key, values.length === 1 ? values[0] : values);
+    }
   }
 
   if (nodeResponse.body) {