diff --git a/api/server/controllers/agents/client.js b/api/server/controllers/agents/client.js
index 31fd56930e..9631fe3801 100644
--- a/api/server/controllers/agents/client.js
+++ b/api/server/controllers/agents/client.js
@@ -32,11 +32,12 @@ const { getCustomEndpointConfig, checkCapability } = require('~/server/services/
 const { addCacheControl, createContextHandlers } = require('~/app/clients/prompts');
 const { spendTokens, spendStructuredTokens } = require('~/models/spendTokens');
 const { getBufferString, HumanMessage } = require('@langchain/core/messages');
+const { DynamicStructuredTool } = require('@langchain/core/tools');
 const { encodeAndFormat } = require('~/server/services/Files/images/encode');
 const initOpenAI = require('~/server/services/Endpoints/openAI/initialize');
 const Tokenizer = require('~/server/services/Tokenizer');
 const BaseClient = require('~/app/clients/BaseClient');
-const { logger, sendEvent } = require('~/config');
+const { logger, sendEvent, getMCPManager } = require('~/config');
 const { createRun } = require('./run');
 
 /**
@@ -370,6 +371,37 @@ class AgentClient extends BaseClient {
       systemContent = this.augmentedPrompt + systemContent;
     }
 
+    // Inject MCP server instructions if available
+    const ephemeralAgent = this.options.req.body.ephemeralAgent;
+    let mcpServers = [];
+
+    // Check for ephemeral agent MCP servers
+    if (ephemeralAgent && ephemeralAgent.mcp && ephemeralAgent.mcp.length > 0) {
+      mcpServers = ephemeralAgent.mcp;
+    }
+    // Check for regular agent MCP tools
+    else if (this.options.agent && this.options.agent.tools) {
+      mcpServers = this.options.agent.tools
+        .filter(
+          (tool) =>
+            tool instanceof DynamicStructuredTool && tool.name.includes(Constants.mcp_delimiter),
+        )
+        .map((tool) => tool.name.split(Constants.mcp_delimiter).pop())
+        .filter(Boolean);
+    }
+
+    if (mcpServers.length > 0) {
+      try {
+        const mcpInstructions = await getMCPManager().formatInstructionsForContext(mcpServers);
+        if (mcpInstructions) {
+          systemContent = [systemContent, mcpInstructions].filter(Boolean).join('\n\n');
+          logger.debug('[AgentClient] Injected MCP instructions for servers:', mcpServers);
+        }
+      } catch (error) {
+        logger.error('[AgentClient] Failed to inject MCP instructions:', error);
+      }
+    }
+
     if (systemContent) {
       this.options.agent.instructions = systemContent;
     }
diff --git a/packages/data-provider/src/mcp.ts b/packages/data-provider/src/mcp.ts
index 258eb15ae3..1273274c54 100644
--- a/packages/data-provider/src/mcp.ts
+++ b/packages/data-provider/src/mcp.ts
@@ -7,6 +7,13 @@ const BaseOptionsSchema = z.object({
   initTimeout: z.number().optional(),
   /** Controls visibility in chat dropdown menu (MCPSelect) */
   chatMenu: z.boolean().optional(),
+  /** 
+   * Controls server instruction behavior:
+   * - undefined/not set: No instructions included (default)
+   * - true: Use server-provided instructions
+   * - string: Use custom instructions (overrides server-provided)
+   */
+  serverInstructions: z.union([z.boolean(), z.string()]).optional(),
 });
 
 export const StdioOptionsSchema = BaseOptionsSchema.extend({
diff --git a/packages/mcp/src/manager.ts b/packages/mcp/src/manager.ts
index 8fe9074b8f..0d8a1e4653 100644
--- a/packages/mcp/src/manager.ts
+++ b/packages/mcp/src/manager.ts
@@ -22,6 +22,8 @@ export class MCPManager {
   private readonly USER_CONNECTION_IDLE_TIMEOUT = 15 * 60 * 1000; // 15 minutes (TODO: make configurable)
   private mcpConfigs: t.MCPServers = {};
   private processMCPEnv?: (obj: MCPOptions, userId?: string) => MCPOptions; // Store the processing function
+  /** Store MCP server instructions */
+  private serverInstructions: Map<string, string> = new Map();
   private logger: Logger;
 
   private static getDefaultLogger(): Logger {
@@ -75,6 +77,42 @@ export class MCPManager {
             initializedServers.add(i);
             this.connections.set(serverName, connection); // Store in app-level map
 
+            // Handle unified serverInstructions configuration
+            const configInstructions = config.serverInstructions;
+
+            if (configInstructions !== undefined) {
+              if (typeof configInstructions === 'string') {
+                // Custom instructions provided
+                this.serverInstructions.set(serverName, configInstructions);
+                this.logger.info(
+                  `[MCP][${serverName}] Custom instructions stored for context inclusion: ${configInstructions}`,
+                );
+              } else if (configInstructions === true) {
+                // Use server-provided instructions
+                const serverInstructions = connection.client.getInstructions();
+
+                if (serverInstructions) {
+                  this.serverInstructions.set(serverName, serverInstructions);
+                  this.logger.info(
+                    `[MCP][${serverName}] Server instructions stored for context inclusion: ${serverInstructions}`,
+                  );
+                } else {
+                  this.logger.info(
+                    `[MCP][${serverName}] serverInstructions=true but no server instructions available`,
+                  );
+                }
+              } else {
+                // configInstructions is false - explicitly disabled
+                this.logger.info(
+                  `[MCP][${serverName}] Instructions explicitly disabled (serverInstructions=false)`,
+                );
+              }
+            } else {
+              this.logger.info(
+                `[MCP][${serverName}] Instructions not included (serverInstructions not configured)`,
+              );
+            }
+
             const serverCapabilities = connection.client.getServerCapabilities();
             this.logger.info(
               `[MCP][${serverName}] Capabilities: ${JSON.stringify(serverCapabilities)}`,
@@ -519,4 +557,61 @@ export class MCPManager {
       logger.info('[MCP] Manager instance destroyed.');
     }
   }
+
+  /**
+   * Get instructions for MCP servers
+   * @param serverNames Optional array of server names. If not provided or empty, returns all servers.
+   * @returns Object mapping server names to their instructions
+   */
+  public getInstructions(serverNames?: string[]): Record<string, string> {
+    const instructions: Record<string, string> = {};
+
+    if (!serverNames || serverNames.length === 0) {
+      // Return all instructions if no specific servers requested
+      for (const [serverName, serverInstructions] of this.serverInstructions.entries()) {
+        instructions[serverName] = serverInstructions;
+      }
+    } else {
+      // Return instructions for specific servers
+      for (const serverName of serverNames) {
+        const serverInstructions = this.serverInstructions.get(serverName);
+        if (serverInstructions) {
+          instructions[serverName] = serverInstructions;
+        }
+      }
+    }
+
+    return instructions;
+  }
+
+  /**
+   * Format MCP server instructions for injection into context
+   * @param serverNames Optional array of server names to include. If not provided, includes all servers.
+   * @returns Formatted instructions string ready for context injection
+   */
+  public formatInstructionsForContext(serverNames?: string[]): string {
+    /** Instructions for specified servers or all stored instructions */
+    const instructionsToInclude = this.getInstructions(serverNames);
+
+    if (Object.keys(instructionsToInclude).length === 0) {
+      return '';
+    }
+
+    // Format instructions for context injection
+    const formattedInstructions = Object.entries(instructionsToInclude)
+      .map(([serverName, instructions]) => {
+        return `## ${serverName} MCP Server Instructions
+
+${instructions}`;
+      })
+      .join('\n\n');
+
+    return `# MCP Server Instructions
+
+The following MCP servers are available with their specific instructions:
+
+${formattedInstructions}
+
+Please follow these instructions when using tools from the respective MCP servers.`;
+  }
 }