diff --git a/server/src/index.ts b/server/src/index.ts
index c0fb3797a..3f739f39e 100644
--- a/server/src/index.ts
+++ b/server/src/index.ts
@@ -22,12 +22,6 @@ import mcpProxy from "./mcpProxy.js";
 import { randomUUID, randomBytes, timingSafeEqual } from "node:crypto";
 
 const DEFAULT_MCP_PROXY_LISTEN_PORT = "6277";
-const SSE_HEADERS_PASSTHROUGH = ["authorization"];
-const STREAMABLE_HTTP_HEADERS_PASSTHROUGH = [
-  "authorization",
-  "mcp-session-id",
-  "last-event-id",
-];
 
 const defaultEnvironment = {
   ...getDefaultEnvironment(),
@@ -46,43 +40,84 @@ const { values } = parseArgs({
 });
 
 // Function to get HTTP headers.
-// Supports only "sse" and "streamable-http" transport types.
-const getHttpHeaders = (
-  req: express.Request,
-  transportType: string,
-): HeadersInit => {
-  const headers: HeadersInit = {
-    Accept:
-      transportType === "sse"
-        ? "text/event-stream"
-        : "text/event-stream, application/json",
-  };
-  const defaultHeaders =
-    transportType === "sse"
-      ? SSE_HEADERS_PASSTHROUGH
-      : STREAMABLE_HTTP_HEADERS_PASSTHROUGH;
-
-  for (const key of defaultHeaders) {
-    if (req.headers[key] === undefined) {
-      continue;
+const getHttpHeaders = (req: express.Request): Record<string, string> => {
+  const headers: Record<string, string> = {};
+
+  // Iterate over all headers in the request
+  for (const key in req.headers) {
+    const lowerKey = key.toLowerCase();
+
+    // Check if the header is one we want to forward
+    if (
+      lowerKey.startsWith("mcp-") ||
+      lowerKey === "authorization" ||
+      lowerKey === "last-event-id"
+    ) {
+      // Exclude the proxy's own authentication header
+      if (lowerKey !== "x-mcp-proxy-auth") {
+        const value = req.headers[key];
+
+        if (typeof value === "string") {
+          // If the value is a string, use it directly
+          headers[key] = value;
+        } else if (Array.isArray(value)) {
+          // If the value is an array, use the last element
+          const lastValue = value.at(-1);
+          if (lastValue !== undefined) {
+            headers[key] = lastValue;
+          }
+        }
+        // If value is undefined, it's skipped, which is correct.
+      }
     }
-
-    const value = req.headers[key];
-    headers[key] = Array.isArray(value) ? value[value.length - 1] : value;
   }
 
-  // If the header "x-custom-auth-header" is present, use its value as the custom header name.
-  if (req.headers["x-custom-auth-header"] !== undefined) {
-    const customHeaderName = req.headers["x-custom-auth-header"] as string;
-    const lowerCaseHeaderName = customHeaderName.toLowerCase();
-    if (req.headers[lowerCaseHeaderName] !== undefined) {
-      const value = req.headers[lowerCaseHeaderName];
-      headers[customHeaderName] = value as string;
+  // Handle the custom auth header separately. We expect `x-custom-auth-header`
+  // to be a string containing the name of the actual authentication header.
+  const customAuthHeaderName = req.headers["x-custom-auth-header"];
+  if (typeof customAuthHeaderName === "string") {
+    const lowerCaseHeaderName = customAuthHeaderName.toLowerCase();
+    const value = req.headers[lowerCaseHeaderName];
+
+    if (typeof value === "string") {
+      headers[customAuthHeaderName] = value;
+    } else if (Array.isArray(value)) {
+      // If the actual auth header was sent multiple times, use the last value.
+      const lastValue = value.at(-1);
+      if (lastValue !== undefined) {
+        headers[customAuthHeaderName] = lastValue;
+      }
     }
   }
+
   return headers;
 };
 
+/**
+ * Updates a headers object in-place, preserving the original Accept header.
+ * This is necessary to ensure that transports holding a reference to the headers
+ * object see the updates.
+ * @param currentHeaders The headers object to update.
+ * @param newHeaders The new headers to apply.
+ */
+const updateHeadersInPlace = (
+  currentHeaders: Record<string, string>,
+  newHeaders: Record<string, string>,
+) => {
+  // Preserve the Accept header, which is set at transport creation and
+  // is not present in subsequent client requests.
+  const accept = currentHeaders["Accept"];
+
+  // Clear the old headers and apply the new ones.
+  Object.keys(currentHeaders).forEach((key) => delete currentHeaders[key]);
+  Object.assign(currentHeaders, newHeaders);
+
+  // Restore the Accept header.
+  if (accept) {
+    currentHeaders["Accept"] = accept;
+  }
+};
+
 const app = express();
 app.use(cors());
 app.use((req, res, next) => {
@@ -92,6 +127,7 @@ app.use((req, res, next) => {
 
 const webAppTransports: Map<string, Transport> = new Map<string, Transport>(); // Web app transports by web app sessionId
 const serverTransports: Map<string, Transport> = new Map<string, Transport>(); // Server Transports by web app sessionId
+const sessionHeaderHolders: Map<string, { headers: HeadersInit }> = new Map(); // For dynamic header updates
 
 // Use provided token from environment or generate a new one
 const sessionToken =
@@ -174,7 +210,38 @@ const authMiddleware = (
   next();
 };
 
-const createTransport = async (req: express.Request): Promise<Transport> => {
+/**
+ * Creates a `fetch` function that merges dynamic session headers with the
+ * headers from the actual request, ensuring that request-specific headers like
+ * `Content-Type` are preserved.
+ */
+const createCustomFetch = (headerHolder: { headers: HeadersInit }) => {
+  return (input: RequestInfo | URL, init?: RequestInit): Promise<Response> => {
+    // Determine the headers from the original request/init.
+    // The SDK may pass a Request object or a URL and an init object.
+    const originalHeaders =
+      input instanceof Request ? input.headers : init?.headers;
+
+    // Start with our dynamic session headers.
+    const finalHeaders = new Headers(headerHolder.headers);
+
+    // Merge the SDK's request-specific headers, letting them overwrite.
+    // This is crucial for preserving Content-Type on POST requests.
+    new Headers(originalHeaders).forEach((value, key) => {
+      finalHeaders.set(key, value);
+    });
+
+    // This works for both `fetch(url, init)` and `fetch(request)` style calls.
+    return fetch(input, { ...init, headers: finalHeaders });
+  };
+};
+
+const createTransport = async (
+  req: express.Request,
+): Promise<{
+  transport: Transport;
+  headerHolder?: { headers: HeadersInit };
+}> => {
   const query = req.query;
   console.log("Query parameters:", JSON.stringify(query));
 
@@ -198,11 +265,13 @@ const createTransport = async (req: express.Request): Promise<Transport> => {
     });
 
     await transport.start();
-    return transport;
+    return { transport };
   } else if (transportType === "sse") {
     const url = query.url as string;
 
-    const headers = getHttpHeaders(req, transportType);
+    const headers = getHttpHeaders(req);
+    headers["Accept"] = "text/event-stream";
+    const headerHolder = { headers };
 
     console.log(
       `SSE transport: url=${url}, headers=${JSON.stringify(headers)}`,
@@ -210,27 +279,28 @@ const createTransport = async (req: express.Request): Promise<Transport> => {
 
     const transport = new SSEClientTransport(new URL(url), {
       eventSourceInit: {
-        fetch: (url, init) => fetch(url, { ...init, headers }),
+        fetch: createCustomFetch(headerHolder),
       },
       requestInit: {
-        headers,
+        headers: headerHolder.headers,
       },
     });
     await transport.start();
-    return transport;
+    return { transport, headerHolder };
   } else if (transportType === "streamable-http") {
-    const headers = getHttpHeaders(req, transportType);
+    const headers = getHttpHeaders(req);
+    headers["Accept"] = "text/event-stream, application/json";
+    const headerHolder = { headers };
 
     const transport = new StreamableHTTPClientTransport(
       new URL(query.url as string),
       {
-        requestInit: {
-          headers,
-        },
+        // Pass a custom fetch to inject the latest headers on each request
+        fetch: createCustomFetch(headerHolder),
       },
     );
     await transport.start();
-    return transport;
+    return { transport, headerHolder };
   } else {
     console.error(`Invalid transport type: ${transportType}`);
     throw new Error("Invalid transport type specified");
@@ -244,6 +314,15 @@ app.get(
   async (req, res) => {
     const sessionId = req.headers["mcp-session-id"] as string;
     console.log(`Received GET message for sessionId ${sessionId}`);
+
+    const headerHolder = sessionHeaderHolders.get(sessionId);
+    if (headerHolder) {
+      updateHeadersInPlace(
+        headerHolder.headers as Record<string, string>,
+        getHttpHeaders(req),
+      );
+    }
+
     try {
       const transport = webAppTransports.get(
         sessionId,
@@ -267,34 +346,54 @@ app.post(
   authMiddleware,
   async (req, res) => {
     const sessionId = req.headers["mcp-session-id"] as string | undefined;
-    let serverTransport: Transport | undefined;
-    if (!sessionId) {
-      try {
-        console.log("New StreamableHttp connection request");
-        try {
-          serverTransport = await createTransport(req);
-        } catch (error) {
-          if (error instanceof SseError && error.code === 401) {
-            console.error(
-              "Received 401 Unauthorized from MCP server:",
-              error.message,
-            );
-            res.status(401).json(error);
-            return;
-          }
 
-          throw error;
-        }
+    if (sessionId) {
+      console.log(`Received POST message for sessionId ${sessionId}`);
+      const headerHolder = sessionHeaderHolders.get(sessionId);
+      if (headerHolder) {
+        updateHeadersInPlace(
+          headerHolder.headers as Record<string, string>,
+          getHttpHeaders(req),
+        );
+      }
 
-        console.log("Created StreamableHttp server transport");
+      try {
+        const transport = webAppTransports.get(
+          sessionId,
+        ) as StreamableHTTPServerTransport;
+        if (!transport) {
+          res.status(404).end("Transport not found for sessionId " + sessionId);
+        } else {
+          await (transport as StreamableHTTPServerTransport).handleRequest(
+            req,
+            res,
+          );
+        }
+      } catch (error) {
+        console.error("Error in /mcp route:", error);
+        res.status(500).json(error);
+      }
+    } else {
+      console.log("New StreamableHttp connection request");
+      try {
+        const { transport: serverTransport, headerHolder } =
+          await createTransport(req);
 
         const webAppTransport = new StreamableHTTPServerTransport({
           sessionIdGenerator: randomUUID,
           onsessioninitialized: (sessionId) => {
             webAppTransports.set(sessionId, webAppTransport);
-            serverTransports.set(sessionId, serverTransport!);
+            serverTransports.set(sessionId, serverTransport!); // eslint-disable-line @typescript-eslint/no-non-null-assertion
+            if (headerHolder) {
+              sessionHeaderHolders.set(sessionId, headerHolder);
+            }
             console.log("Client <-> Proxy  sessionId: " + sessionId);
           },
+          onsessionclosed: (sessionId) => {
+            webAppTransports.delete(sessionId);
+            serverTransports.delete(sessionId);
+            sessionHeaderHolders.delete(sessionId);
+          },
         });
         console.log("Created StreamableHttp client transport");
 
@@ -311,25 +410,15 @@ app.post(
           req.body,
         );
       } catch (error) {
-        console.error("Error in /mcp POST route:", error);
-        res.status(500).json(error);
-      }
-    } else {
-      console.log(`Received POST message for sessionId ${sessionId}`);
-      try {
-        const transport = webAppTransports.get(
-          sessionId,
-        ) as StreamableHTTPServerTransport;
-        if (!transport) {
-          res.status(404).end("Transport not found for sessionId " + sessionId);
-        } else {
-          await (transport as StreamableHTTPServerTransport).handleRequest(
-            req,
-            res,
+        if (error instanceof SseError && error.code === 401) {
+          console.error(
+            "Received 401 Unauthorized from MCP server:",
+            error.message,
           );
+          res.status(401).json(error);
+          return;
         }
-      } catch (error) {
-        console.error("Error in /mcp route:", error);
+        console.error("Error in /mcp POST route:", error);
         res.status(500).json(error);
       }
     }
@@ -343,20 +432,18 @@ app.delete(
   async (req, res) => {
     const sessionId = req.headers["mcp-session-id"] as string | undefined;
     console.log(`Received DELETE message for sessionId ${sessionId}`);
-    let serverTransport: Transport | undefined;
     if (sessionId) {
       try {
-        serverTransport = serverTransports.get(
+        const serverTransport = serverTransports.get(
           sessionId,
         ) as StreamableHTTPClientTransport;
         if (!serverTransport) {
           res.status(404).end("Transport not found for sessionId " + sessionId);
         } else {
-          await (
-            serverTransport as StreamableHTTPClientTransport
-          ).terminateSession();
+          await serverTransport.terminateSession();
           webAppTransports.delete(sessionId);
           serverTransports.delete(sessionId);
+          sessionHeaderHolders.delete(sessionId);
           console.log(`Transports removed for sessionId ${sessionId}`);
         }
         res.status(200).end();
@@ -375,20 +462,7 @@ app.get(
   async (req, res) => {
     try {
       console.log("New STDIO connection request");
-      let serverTransport: Transport | undefined;
-      try {
-        serverTransport = await createTransport(req);
-      } catch (error) {
-        if (error instanceof SseError && error.code === 401) {
-          console.error(
-            "Received 401 Unauthorized from MCP server. Authentication failure.",
-          );
-          res.status(401).json(error);
-          return;
-        }
-
-        throw error;
-      }
+      const { transport: serverTransport } = await createTransport(req);
 
       const proxyFullAddress = (req.query.proxyFullAddress as string) || "";
       const prefix = proxyFullAddress || "";
@@ -422,6 +496,7 @@ app.get(
           serverTransport.close();
           webAppTransports.delete(webAppTransport.sessionId);
           serverTransports.delete(webAppTransport.sessionId);
+          sessionHeaderHolders.delete(webAppTransport.sessionId);
           console.error(message);
         } else {
           // Inspect message and attempt to assign a RFC 5424 Syslog Protocol level
@@ -475,6 +550,13 @@ app.get(
         transportToServer: serverTransport,
       });
     } catch (error) {
+      if (error instanceof SseError && error.code === 401) {
+        console.error(
+          "Received 401 Unauthorized from MCP server. Authentication failure.",
+        );
+        res.status(401).json(error);
+        return;
+      }
       console.error("Error in /stdio route:", error);
       res.status(500).json(error);
     }
@@ -490,50 +572,46 @@ app.get(
       console.log(
         "New SSE connection request. NOTE: The SSE transport is deprecated and has been replaced by StreamableHttp",
       );
-      let serverTransport: Transport | undefined;
-      try {
-        serverTransport = await createTransport(req);
-      } catch (error) {
-        if (error instanceof SseError && error.code === 401) {
-          console.error(
-            "Received 401 Unauthorized from MCP server. Authentication failure.",
-          );
-          res.status(401).json(error);
-          return;
-        } else if (error instanceof SseError && error.code === 404) {
-          console.error(
-            "Received 404 not found from MCP server. Does the MCP server support SSE?",
-          );
-          res.status(404).json(error);
-          return;
-        } else if (JSON.stringify(error).includes("ECONNREFUSED")) {
-          console.error("Connection refused. Is the MCP server running?");
-          res.status(500).json(error);
-        } else {
-          throw error;
-        }
-      }
+      const { transport: serverTransport, headerHolder } =
+        await createTransport(req);
 
-      if (serverTransport) {
-        const proxyFullAddress = (req.query.proxyFullAddress as string) || "";
-        const prefix = proxyFullAddress || "";
-        const endpoint = `${prefix}/message`;
+      const proxyFullAddress = (req.query.proxyFullAddress as string) || "";
+      const prefix = proxyFullAddress || "";
+      const endpoint = `${prefix}/message`;
 
-        const webAppTransport = new SSEServerTransport(endpoint, res);
-        webAppTransports.set(webAppTransport.sessionId, webAppTransport);
-        console.log("Created client transport");
+      const webAppTransport = new SSEServerTransport(endpoint, res);
+      webAppTransports.set(webAppTransport.sessionId, webAppTransport);
+      console.log("Created client transport");
 
-        serverTransports.set(webAppTransport.sessionId, serverTransport!);
-        console.log("Created server transport");
+      serverTransports.set(webAppTransport.sessionId, serverTransport!); // eslint-disable-line @typescript-eslint/no-non-null-assertion
+      if (headerHolder) {
+        sessionHeaderHolders.set(webAppTransport.sessionId, headerHolder);
+      }
+      console.log("Created server transport");
 
-        await webAppTransport.start();
+      await webAppTransport.start();
 
-        mcpProxy({
-          transportToClient: webAppTransport,
-          transportToServer: serverTransport,
-        });
-      }
+      mcpProxy({
+        transportToClient: webAppTransport,
+        transportToServer: serverTransport,
+      });
     } catch (error) {
+      if (error instanceof SseError && error.code === 401) {
+        console.error(
+          "Received 401 Unauthorized from MCP server. Authentication failure.",
+        );
+        res.status(401).json(error);
+        return;
+      } else if (error instanceof SseError && error.code === 404) {
+        console.error(
+          "Received 404 not found from MCP server. Does the MCP server support SSE?",
+        );
+        res.status(404).json(error);
+        return;
+      } else if (JSON.stringify(error).includes("ECONNREFUSED")) {
+        console.error("Connection refused. Is the MCP server running?");
+        res.status(500).json(error);
+      }
       console.error("Error in /sse route:", error);
       res.status(500).json(error);
     }
@@ -546,12 +624,18 @@ app.post(
   authMiddleware,
   async (req, res) => {
     try {
-      const sessionId = req.query.sessionId;
+      const sessionId = req.query.sessionId as string;
       console.log(`Received POST message for sessionId ${sessionId}`);
 
-      const transport = webAppTransports.get(
-        sessionId as string,
-      ) as SSEServerTransport;
+      const headerHolder = sessionHeaderHolders.get(sessionId);
+      if (headerHolder) {
+        updateHeadersInPlace(
+          headerHolder.headers as Record<string, string>,
+          getHttpHeaders(req),
+        );
+      }
+
+      const transport = webAppTransports.get(sessionId) as SSEServerTransport;
       if (!transport) {
         res.status(404).end("Session not found");
         return;