diff --git a/src/client.ts b/src/client.ts
index 50731cf..81310b7 100644
--- a/src/client.ts
+++ b/src/client.ts
@@ -329,15 +329,38 @@ function createStdioTransport(config: StdioServerConfig): StdioClientTransport {
 
 /**
  * List all tools from a connected client with retry logic
+ * Follows MCP pagination cursors until all tool pages are fetched.
  */
 export async function listTools(client: Client): Promise<ToolInfo[]> {
   return withRetry(async () => {
-    const result = await client.listTools();
-    return result.tools.map((tool: Tool) => ({
-      name: tool.name,
-      description: tool.description,
-      inputSchema: tool.inputSchema as Record<string, unknown>,
-    }));
+    const tools: ToolInfo[] = [];
+    const seenCursors = new Set<string>();
+    let cursor: string | undefined;
+
+    while (true) {
+      const result = await client.listTools(cursor ? { cursor } : undefined);
+
+      tools.push(
+        ...result.tools.map((tool: Tool) => ({
+          name: tool.name,
+          description: tool.description,
+          inputSchema: tool.inputSchema as Record<string, unknown>,
+        })),
+      );
+
+      if (!result.nextCursor) {
+        return tools;
+      }
+
+      if (seenCursors.has(result.nextCursor)) {
+        throw new Error(
+          `listTools pagination loop detected at cursor: ${result.nextCursor}`,
+        );
+      }
+
+      seenCursors.add(result.nextCursor);
+      cursor = result.nextCursor;
+    }
   }, 'list tools');
 }
 
diff --git a/src/config.ts b/src/config.ts
index 99a4e25..59e2366 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -496,9 +496,6 @@ export async function loadConfig(
     }
   }
 
-  // Substitute environment variables
-  config = substituteEnvVarsInObject(config);
-
   return config;
 }
 
@@ -514,7 +511,7 @@ export function getServerConfig(
     const available = Object.keys(config.mcpServers);
     throw new Error(formatCliError(serverNotFoundError(serverName, available)));
   }
-  return server;
+  return substituteEnvVarsInObject(server);
 }
 
 /**
diff --git a/tests/client.test.ts b/tests/client.test.ts
index 9c53200..643c000 100644
--- a/tests/client.test.ts
+++ b/tests/client.test.ts
@@ -15,6 +15,7 @@ import {
   isTransientError,
   getTimeoutMs,
   getConcurrencyLimit,
+  listTools,
 } from '../src/client';
 
 describe('client', () => {
@@ -240,6 +241,61 @@ describe('client', () => {
     });
   });
 
+  describe('listTools', () => {
+    test('collects all tool pages when server returns nextCursor', async () => {
+      const calls: Array<string | undefined> = [];
+      const client = {
+        listTools: async (params?: { cursor?: string }) => {
+          calls.push(params?.cursor);
+
+          if (!params?.cursor) {
+            return {
+              tools: [
+                {
+                  name: 'tool-a',
+                  inputSchema: { type: 'object' },
+                },
+              ],
+              nextCursor: 'page-2',
+            };
+          }
+
+          return {
+            tools: [
+              {
+                name: 'tool-b',
+                inputSchema: { type: 'object' },
+              },
+            ],
+          };
+        },
+      } as any;
+
+      const tools = await listTools(client);
+
+      expect(calls).toEqual([undefined, 'page-2']);
+      expect(tools.map((tool) => tool.name)).toEqual(['tool-a', 'tool-b']);
+    });
+
+    test('throws when paginated listTools repeats the same cursor', async () => {
+      const client = {
+        listTools: async () => ({
+          tools: [
+            {
+              name: 'tool-a',
+              inputSchema: { type: 'object' },
+            },
+          ],
+          nextCursor: 'stuck',
+        }),
+      } as any;
+
+      await expect(listTools(client)).rejects.toThrow(
+        'pagination loop detected',
+      );
+    });
+  });
+
   // Note: Actually testing connectToServer requires a real MCP server
   // Those tests are in the integration test suite
 });
diff --git a/tests/config.test.ts b/tests/config.test.ts
index a48602c..0165f0d 100644
--- a/tests/config.test.ts
+++ b/tests/config.test.ts
@@ -61,7 +61,7 @@ describe('config', () => {
       await expect(loadConfig(configPath)).rejects.toThrow('mcpServers');
     });
 
-    test('substitutes environment variables', async () => {
+    test('loads config without eagerly substituting environment variables', async () => {
       process.env.TEST_MCP_TOKEN = 'secret123';
 
       const configPath = join(tempDir, 'env_config.json');
@@ -79,11 +79,35 @@ describe('config', () => {
 
       const config = await loadConfig(configPath);
       const server = config.mcpServers.test as any;
-      expect(server.headers.Authorization).toBe('Bearer secret123');
+      expect(server.headers.Authorization).toBe('Bearer ${TEST_MCP_TOKEN}');
 
       delete process.env.TEST_MCP_TOKEN;
     });
 
+    test('does not throw for unrelated servers with missing env vars', async () => {
+      delete process.env.UNRELATED_MISSING_VAR;
+
+      const configPath = join(tempDir, 'scoped_env_config.json');
+      await writeFile(
+        configPath,
+        JSON.stringify({
+          mcpServers: {
+            safe: {
+              command: 'echo',
+            },
+            noisy: {
+              command: 'echo',
+              env: { TOKEN: '${UNRELATED_MISSING_VAR}' },
+            },
+          },
+        })
+      );
+
+      const config = await loadConfig(configPath);
+      expect(() => getServerConfig(config, 'safe')).not.toThrow();
+      expect(() => getServerConfig(config, 'noisy')).toThrow('MISSING_ENV_VAR');
+    });
+
     test('handles missing env vars gracefully with MCP_STRICT_ENV=false', async () => {
       // Set non-strict mode to allow missing env vars with warning
       process.env.MCP_STRICT_ENV = 'false';
@@ -102,12 +126,35 @@ describe('config', () => {
       );
 
       const config = await loadConfig(configPath);
-      const server = config.mcpServers.test as any;
+      const server = getServerConfig(config, 'test') as any;
       expect(server.env.TOKEN).toBe('');
 
       delete process.env.MCP_STRICT_ENV;
     });
 
+
+    test('treats MCP_STRICT_ENV with surrounding-CRLF trailing-tab true as strict mode', async () => {
+      process.env.MCP_STRICT_ENV = '\r\ntrue\t\r\n';
+
+      const configPath = join(tempDir, 'missing_env_trailing_tab_true_surrounded_crlf.json');
+      await writeFile(
+        configPath,
+        JSON.stringify({
+          mcpServers: {
+            test: {
+              command: 'echo',
+              env: { TOKEN: '${NONEXISTENT_VAR}' },
+            },
+          },
+        })
+      );
+
+      const config = await loadConfig(configPath);
+      expect(() => getServerConfig(config, 'test')).toThrow('Missing environment variable');
+
+      delete process.env.MCP_STRICT_ENV;
+    });
+
     test('throws error on missing env vars in strict mode (default)', async () => {
       // Ensure strict mode is enabled (default)
       delete process.env.MCP_STRICT_ENV;
@@ -125,7 +172,8 @@ describe('config', () => {
         })
       );
 
-      await expect(loadConfig(configPath)).rejects.toThrow('MISSING_ENV_VAR');
+      const config = await loadConfig(configPath);
+      expect(() => getServerConfig(config, 'test')).toThrow('MISSING_ENV_VAR');
     });
 
     test('throws error on empty server config', async () => {