diff --git a/pkg/agent/loop_mcp.go b/pkg/agent/loop_mcp.go
index 1fad059a4..c9f3bc03d 100644
--- a/pkg/agent/loop_mcp.go
+++ b/pkg/agent/loop_mcp.go
@@ -69,8 +69,18 @@ func (al *AgentLoop) ensureMCPInitialized(ctx context.Context) error {
 		return nil
 	}
 
+	mcpCfg := filterMCPConfigServers(al.cfg.Tools.MCP, al.registry.allowedMCPServers())
+	if mcpCfg.Servers == nil || len(mcpCfg.Servers) == 0 {
+		logger.InfoCF(
+			"agent",
+			"No MCP servers selected after applying per-agent mcpServers allowlists",
+			nil,
+		)
+		return nil
+	}
+
 	findValidServer := false
-	for _, serverCfg := range al.cfg.Tools.MCP.Servers {
+	for _, serverCfg := range mcpCfg.Servers {
 		if serverCfg.Enabled {
 			findValidServer = true
 		}
@@ -89,7 +99,7 @@ func (al *AgentLoop) ensureMCPInitialized(ctx context.Context) error {
 			workspacePath = defaultAgent.Workspace
 		}
 
-		if err := mcpManager.LoadFromMCPConfig(ctx, al.cfg.Tools.MCP, workspacePath); err != nil {
+		if err := mcpManager.LoadFromMCPConfig(ctx, mcpCfg, workspacePath); err != nil {
 			logger.WarnCF("agent", "Failed to load MCP servers, MCP tools will not be available",
 				map[string]any{
 					"error": err.Error(),
@@ -115,7 +125,7 @@ func (al *AgentLoop) ensureMCPInitialized(ctx context.Context) error {
 
 			// Determine whether this server's tools should be deferred (hidden).
 			// Per-server "deferred" field takes precedence over the global Discovery.Enabled.
-			serverCfg := al.cfg.Tools.MCP.Servers[serverName]
+			serverCfg := mcpCfg.Servers[serverName]
 			registerAsHidden := serverIsDeferred(al.cfg.Tools.MCP.Discovery.Enabled, serverCfg)
 
 			for _, tool := range conn.Tools {
@@ -216,6 +226,25 @@ func (al *AgentLoop) ensureMCPInitialized(ctx context.Context) error {
 	return al.mcp.getInitErr()
 }
 
+func filterMCPConfigServers(
+	mcpCfg config.MCPConfig,
+	allowed map[string]struct{},
+) config.MCPConfig {
+	if allowed == nil {
+		return mcpCfg
+	}
+
+	filtered := mcpCfg
+	filtered.Servers = make(map[string]config.MCPServerConfig)
+	for serverName, serverCfg := range mcpCfg.Servers {
+		if _, ok := allowed[serverName]; ok {
+			filtered.Servers[serverName] = serverCfg
+		}
+	}
+
+	return filtered
+}
+
 // serverIsDeferred reports whether an MCP server's tools should be registered
 // as hidden (deferred/discovery mode).
 //
diff --git a/pkg/agent/loop_mcp_test.go b/pkg/agent/loop_mcp_test.go
index baf126bd1..ee00d22ba 100644
--- a/pkg/agent/loop_mcp_test.go
+++ b/pkg/agent/loop_mcp_test.go
@@ -122,3 +122,59 @@ func TestAgentInstance_AllowsMCPServer(t *testing.T) {
 		}
 	})
 }
+
+func TestAgentRegistry_AllowedMCPServers(t *testing.T) {
+	t.Run("returns nil when any agent allows all servers", func(t *testing.T) {
+		registry := &AgentRegistry{
+			agents: map[string]*AgentInstance{
+				"main":     {ID: "main", MCPServerAllowlist: nil},
+				"research": {ID: "research", MCPServerAllowlist: map[string]struct{}{"github": {}}},
+			},
+		}
+
+		if allowed := registry.allowedMCPServers(); allowed != nil {
+			t.Fatalf("expected nil union when one agent allows all, got %v", allowed)
+		}
+	})
+
+	t.Run("returns union of explicit allowlists", func(t *testing.T) {
+		registry := &AgentRegistry{
+			agents: map[string]*AgentInstance{
+				"main":     {ID: "main", MCPServerAllowlist: map[string]struct{}{"github": {}}},
+				"research": {ID: "research", MCPServerAllowlist: map[string]struct{}{"filesystem": {}}},
+			},
+		}
+
+		allowed := registry.allowedMCPServers()
+		if len(allowed) != 2 {
+			t.Fatalf("len(allowed) = %d, want 2", len(allowed))
+		}
+		if _, ok := allowed["github"]; !ok {
+			t.Fatal("expected github in allowed MCP server union")
+		}
+		if _, ok := allowed["filesystem"]; !ok {
+			t.Fatal("expected filesystem in allowed MCP server union")
+		}
+	})
+}
+
+func TestFilterMCPConfigServers(t *testing.T) {
+	mcpCfg := config.MCPConfig{
+		ToolConfig: config.ToolConfig{Enabled: true},
+		Servers: map[string]config.MCPServerConfig{
+			"github":     {Enabled: true},
+			"filesystem": {Enabled: true},
+		},
+	}
+
+	filtered := filterMCPConfigServers(mcpCfg, map[string]struct{}{"github": {}})
+	if len(filtered.Servers) != 1 {
+		t.Fatalf("len(filtered.Servers) = %d, want 1", len(filtered.Servers))
+	}
+	if _, ok := filtered.Servers["github"]; !ok {
+		t.Fatal("expected github server to remain after filtering")
+	}
+	if _, ok := filtered.Servers["filesystem"]; ok {
+		t.Fatal("expected filesystem server to be removed by filtering")
+	}
+}
diff --git a/pkg/agent/registry.go b/pkg/agent/registry.go
index ef5645e51..1eba72250 100644
--- a/pkg/agent/registry.go
+++ b/pkg/agent/registry.go
@@ -88,6 +88,30 @@ func (r *AgentRegistry) ListAgentIDs() []string {
 	return ids
 }
 
+func (r *AgentRegistry) allowedMCPServers() map[string]struct{} {
+	r.mu.RLock()
+	defer r.mu.RUnlock()
+
+	if len(r.agents) == 0 {
+		return nil
+	}
+
+	union := make(map[string]struct{})
+	for _, agent := range r.agents {
+		if agent == nil {
+			continue
+		}
+		if agent.MCPServerAllowlist == nil {
+			return nil
+		}
+		for serverName := range agent.MCPServerAllowlist {
+			union[serverName] = struct{}{}
+		}
+	}
+
+	return union
+}
+
 // CanSpawnSubagent checks if parentAgentID is allowed to spawn targetAgentID.
 func (r *AgentRegistry) CanSpawnSubagent(parentAgentID, targetAgentID string) bool {
 	parent, ok := r.GetAgent(parentAgentID)