diff --git a/README.md b/README.md
index ca9d961..d95aaaa 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,37 @@ To bypass authentication, or to emit custom headers on all requests to your remo
 },
 ```
 
+### Multiple Instances
+
+To run multiple instances of the same remote server with different configurations (e.g., different Atlassian tenants), use the `--resource` flag to isolate OAuth sessions:
+
+```json
+{
+  "mcpServers": {
+    "atlassian_tenant1": {
+      "command": "npx",
+      "args": [
+        "mcp-remote",
+        "https://mcp.atlassian.com/v1/sse",
+        "--resource",
+        "https://tenant1.atlassian.net/"
+      ]
+    },
+    "atlassian_tenant2": {
+      "command": "npx",
+      "args": [
+        "mcp-remote",
+        "https://mcp.atlassian.com/v1/sse",
+        "--resource",
+        "https://tenant2.atlassian.net/"
+      ]
+    }
+  }
+}
+```
+
+Each unique combination of server URL, resource, and custom headers will maintain separate OAuth sessions and token storage.
+
 ### Flags
 
 * If `npx` is producing errors, consider adding `-y` as the first argument to auto-accept the installation of the `mcp-remote` package.
diff --git a/src/client.ts b/src/client.ts
index 0421729..961cb22 100644
--- a/src/client.ts
+++ b/src/client.ts
@@ -13,15 +13,7 @@ import { EventEmitter } from 'events'
 import { Client } from '@modelcontextprotocol/sdk/client/index.js'
 import { ListResourcesResultSchema, ListToolsResultSchema } from '@modelcontextprotocol/sdk/types.js'
 import { NodeOAuthClientProvider } from './lib/node-oauth-client-provider'
-import {
-  parseCommandLineArgs,
-  setupSignalHandlers,
-  log,
-  MCP_REMOTE_VERSION,
-  getServerUrlHash,
-  connectToRemoteServer,
-  TransportStrategy,
-} from './lib/utils'
+import { parseCommandLineArgs, setupSignalHandlers, log, MCP_REMOTE_VERSION, connectToRemoteServer, TransportStrategy } from './lib/utils'
 import { StaticOAuthClientInformationFull, StaticOAuthClientMetadata } from './lib/types'
 import { createLazyAuthCoordinator } from './lib/coordination'
 
@@ -37,13 +29,11 @@ async function runClient(
   staticOAuthClientMetadata: StaticOAuthClientMetadata,
   staticOAuthClientInfo: StaticOAuthClientInformationFull,
   authTimeoutMs: number,
+  serverUrlHash: string,
 ) {
   // Set up event emitter for auth flow
   const events = new EventEmitter()
 
-  // Get the server URL hash for lockfile operations
-  const serverUrlHash = getServerUrlHash(serverUrl)
-
   // Create a lazy auth coordinator
   const authCoordinator = createLazyAuthCoordinator(serverUrlHash, callbackPort, events, authTimeoutMs)
 
@@ -55,6 +45,7 @@ async function runClient(
     clientName: 'MCP CLI Client',
     staticOAuthClientMetadata,
     staticOAuthClientInfo,
+    serverUrlHash,
   })
 
   // Create the client
@@ -161,7 +152,17 @@ async function runClient(
 // Parse command-line arguments and run the client
 parseCommandLineArgs(process.argv.slice(2), 'Usage: npx tsx client.ts <https://server-url> [callback-port] [--debug]')
   .then(
-    ({ serverUrl, callbackPort, headers, transportStrategy, host, staticOAuthClientMetadata, staticOAuthClientInfo, authTimeoutMs }) => {
+    ({
+      serverUrl,
+      callbackPort,
+      headers,
+      transportStrategy,
+      host,
+      staticOAuthClientMetadata,
+      staticOAuthClientInfo,
+      authTimeoutMs,
+      serverUrlHash,
+    }) => {
       return runClient(
         serverUrl,
         callbackPort,
@@ -171,6 +172,7 @@ parseCommandLineArgs(process.argv.slice(2), 'Usage: npx tsx client.ts <https://s
         staticOAuthClientMetadata,
         staticOAuthClientInfo,
         authTimeoutMs,
+        serverUrlHash,
       )
     },
   )
diff --git a/src/lib/node-oauth-client-provider.ts b/src/lib/node-oauth-client-provider.ts
index c97cec3..26a0c02 100644
--- a/src/lib/node-oauth-client-provider.ts
+++ b/src/lib/node-oauth-client-provider.ts
@@ -9,7 +9,7 @@ import {
 import type { OAuthProviderOptions, StaticOAuthClientMetadata } from './types'
 import { readJsonFile, writeJsonFile, readTextFile, writeTextFile, deleteConfigFile } from './mcp-auth-config'
 import { StaticOAuthClientInformationFull } from './types'
-import { getServerUrlHash, log, debugLog, MCP_REMOTE_VERSION } from './utils'
+import { log, debugLog, MCP_REMOTE_VERSION } from './utils'
 import { sanitizeUrl } from 'strict-url-sanitise'
 import { randomUUID } from 'node:crypto'
 
@@ -34,7 +34,7 @@ export class NodeOAuthClientProvider implements OAuthClientProvider {
    * @param options Configuration options for the provider
    */
   constructor(readonly options: OAuthProviderOptions) {
-    this.serverUrlHash = getServerUrlHash(options.serverUrl)
+    this.serverUrlHash = options.serverUrlHash
     this.callbackPath = options.callbackPath || '/oauth/callback'
     this.clientName = options.clientName || 'MCP CLI Client'
     this.clientUri = options.clientUri || 'https://github.com/modelcontextprotocol/mcp-cli'
diff --git a/src/lib/types.ts b/src/lib/types.ts
index db6a8ab..d9f2a10 100644
--- a/src/lib/types.ts
+++ b/src/lib/types.ts
@@ -29,6 +29,8 @@ export interface OAuthProviderOptions {
   staticOAuthClientInfo?: StaticOAuthClientInformationFull
   /** Resource parameter to send to the authorization server */
   authorizeResource?: string
+  /** Pre-calculated server URL hash for cache isolation */
+  serverUrlHash: string
 }
 
 /**
diff --git a/src/lib/utils.test.ts b/src/lib/utils.test.ts
index 9ae95ca..ddf4d90 100644
--- a/src/lib/utils.test.ts
+++ b/src/lib/utils.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest'
-import { parseCommandLineArgs, shouldIncludeTool, mcpProxy, setupOAuthCallbackServerWithLongPoll } from './utils'
+import { parseCommandLineArgs, shouldIncludeTool, mcpProxy, setupOAuthCallbackServerWithLongPoll, getServerUrlHash } from './utils'
 import { Transport } from '@modelcontextprotocol/sdk/shared/transport.js'
 import { EventEmitter } from 'events'
 import express from 'express'
@@ -915,3 +915,41 @@ describe('setupOAuthCallbackServerWithLongPoll', () => {
     expect(typeof result.waitForAuthCode).toBe('function')
   })
 })
+
+describe('Feature: Server URL Hash Generation', () => {
+  it('Scenario: Generate consistent hash for same config', () => {
+    const hash1 = getServerUrlHash('https://example.com', 'resource1', { Auth: 'token' })
+    const hash2 = getServerUrlHash('https://example.com', 'resource1', { Auth: 'token' })
+    expect(hash1).toBe(hash2)
+  })
+
+  it('Scenario: Generate different hash for different resources', () => {
+    const hash1 = getServerUrlHash('https://example.com', 'resource1')
+    const hash2 = getServerUrlHash('https://example.com', 'resource2')
+    expect(hash1).not.toBe(hash2)
+  })
+
+  it('Scenario: Generate different hash for different headers', () => {
+    const hash1 = getServerUrlHash('https://example.com', '', { Auth: 'token1' })
+    const hash2 = getServerUrlHash('https://example.com', '', { Auth: 'token2' })
+    expect(hash1).not.toBe(hash2)
+  })
+
+  it('Scenario: Handle header key ordering consistently', () => {
+    const hash1 = getServerUrlHash('https://example.com', '', { B: '2', A: '1' })
+    const hash2 = getServerUrlHash('https://example.com', '', { A: '1', B: '2' })
+    expect(hash1).toBe(hash2)
+  })
+
+  it('Scenario: Backward compatible with no resource or headers', () => {
+    const hash1 = getServerUrlHash('https://example.com')
+    const hash2 = getServerUrlHash('https://example.com', '', {})
+    expect(hash1).toBe(hash2)
+  })
+
+  it('Scenario: Empty string resource same as undefined', () => {
+    const hash1 = getServerUrlHash('https://example.com', '')
+    const hash2 = getServerUrlHash('https://example.com')
+    expect(hash1).toBe(hash2)
+  })
+})
diff --git a/src/lib/utils.ts b/src/lib/utils.ts
index 3824903..e48fb0c 100644
--- a/src/lib/utils.ts
+++ b/src/lib/utils.ts
@@ -739,7 +739,8 @@ export async function parseCommandLineArgs(args: string[], usage: string) {
     log(usage)
     process.exit(1)
   }
-  const serverUrlHash = getServerUrlHash(serverUrl)
+  // Calculate hash with all parsed parameters for cache isolation
+  const serverUrlHash = getServerUrlHash(serverUrl, authorizeResource, headers)
 
   // Set server hash globally for debug logging
   global.currentServerUrlHash = serverUrlHash
@@ -800,6 +801,7 @@ export async function parseCommandLineArgs(args: string[], usage: string) {
     authorizeResource,
     ignoredTools,
     authTimeoutMs,
+    serverUrlHash,
   }
 }
 
@@ -824,12 +826,24 @@ export function setupSignalHandlers(cleanup: () => Promise<void>) {
 }
 
 /**
- * Generates a hash for the server URL to use in filenames
- * @param serverUrl The server URL to hash
- * @returns The hashed server URL
+ * Generates a hash for the server URL configuration
+ * Includes resource and headers to isolate OAuth sessions per unique
+ * server configuration (fixes #25: multi-instance support)
+ * @param serverUrl The server URL
+ * @param authorizeResource Optional resource parameter for OAuth
+ * @param headers Optional custom headers
+ * @returns MD5 hash of the configuration
  */
-export function getServerUrlHash(serverUrl: string): string {
-  return crypto.createHash('md5').update(serverUrl).digest('hex')
+export function getServerUrlHash(serverUrl: string, authorizeResource?: string, headers?: Record<string, string>): string {
+  // Include resource and headers in hash to isolate OAuth sessions
+  // per unique server configuration (fixes #25)
+  const parts = [serverUrl]
+  if (authorizeResource) parts.push(authorizeResource)
+  if (headers && Object.keys(headers).length > 0) {
+    const sortedKeys = Object.keys(headers).sort()
+    parts.push(JSON.stringify(headers, sortedKeys))
+  }
+  return crypto.createHash('md5').update(parts.join('|')).digest('hex')
 }
 
 /**
diff --git a/src/proxy.ts b/src/proxy.ts
index a5972eb..6a6ad5b 100644
--- a/src/proxy.ts
+++ b/src/proxy.ts
@@ -11,15 +11,7 @@
 
 import { EventEmitter } from 'events'
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
-import {
-  connectToRemoteServer,
-  log,
-  mcpProxy,
-  parseCommandLineArgs,
-  setupSignalHandlers,
-  getServerUrlHash,
-  TransportStrategy,
-} from './lib/utils'
+import { connectToRemoteServer, log, mcpProxy, parseCommandLineArgs, setupSignalHandlers, TransportStrategy } from './lib/utils'
 import { StaticOAuthClientInformationFull, StaticOAuthClientMetadata } from './lib/types'
 import { NodeOAuthClientProvider } from './lib/node-oauth-client-provider'
 import { createLazyAuthCoordinator } from './lib/coordination'
@@ -38,13 +30,11 @@ async function runProxy(
   authorizeResource: string,
   ignoredTools: string[],
   authTimeoutMs: number,
+  serverUrlHash: string,
 ) {
   // Set up event emitter for auth flow
   const events = new EventEmitter()
 
-  // Get the server URL hash for lockfile operations
-  const serverUrlHash = getServerUrlHash(serverUrl)
-
   // Create a lazy auth coordinator
   const authCoordinator = createLazyAuthCoordinator(serverUrlHash, callbackPort, events, authTimeoutMs)
 
@@ -57,6 +47,7 @@ async function runProxy(
     staticOAuthClientMetadata,
     staticOAuthClientInfo,
     authorizeResource,
+    serverUrlHash,
   })
 
   // Create the STDIO transport for local connections
@@ -160,6 +151,7 @@ parseCommandLineArgs(process.argv.slice(2), 'Usage: npx tsx proxy.ts <https://se
       authorizeResource,
       ignoredTools,
       authTimeoutMs,
+      serverUrlHash,
     }) => {
       return runProxy(
         serverUrl,
@@ -172,6 +164,7 @@ parseCommandLineArgs(process.argv.slice(2), 'Usage: npx tsx proxy.ts <https://se
         authorizeResource,
         ignoredTools,
         authTimeoutMs,
+        serverUrlHash,
       )
     },
   )