diff --git a/internal/agent/coordinator.go b/internal/agent/coordinator.go
index 943c3efc41b33ea9f261b4ffc7256b6f544beff9..985445e1dc0e0263b6faba388888bf30ec3bfb92 100644
--- a/internal/agent/coordinator.go
+++ b/internal/agent/coordinator.go
@@ -20,6 +20,7 @@ import (
 	"github.com/charmbracelet/crush/internal/agent/hyper"
 	"github.com/charmbracelet/crush/internal/agent/prompt"
 	"github.com/charmbracelet/crush/internal/agent/tools"
+	"github.com/charmbracelet/crush/internal/agent/tools/mcp"
 	"github.com/charmbracelet/crush/internal/config"
 	"github.com/charmbracelet/crush/internal/csync"
 	"github.com/charmbracelet/crush/internal/history"
@@ -411,6 +412,11 @@ func (c *coordinator) buildTools(ctx context.Context, agent config.Agent) ([]fan
 		}
 	}
 
+	// Wait for MCP initialization to complete before reading MCP tools.
+	if err := mcp.WaitForInit(ctx); err != nil {
+		return nil, fmt.Errorf("failed to wait for MCP initialization: %w", err)
+	}
+
 	for _, tool := range tools.GetMCPTools(c.permissions, c.cfg.WorkingDir()) {
 		if agent.AllowedMCP == nil {
 			// No MCP restrictions
diff --git a/internal/agent/tools/mcp/init.go b/internal/agent/tools/mcp/init.go
index bb43f7f157dc1cf2d094354a4e709e0beb1f52b6..e1e7d609efc86d0dcb510fa5963552f7d487a134 100644
--- a/internal/agent/tools/mcp/init.go
+++ b/internal/agent/tools/mcp/init.go
@@ -29,6 +29,8 @@ var (
 	sessions = csync.NewMap[string, *mcp.ClientSession]()
 	states   = csync.NewMap[string, ClientInfo]()
 	broker   = pubsub.NewBroker[Event]()
+	initOnce sync.Once
+	initDone = make(chan struct{})
 )
 
 // State represents the current state of an MCP client
@@ -197,6 +199,18 @@ func Initialize(ctx context.Context, permissions permission.Service, cfg *config
 		}(name, m)
 	}
 	wg.Wait()
+	initOnce.Do(func() { close(initDone) })
+}
+
+// WaitForInit blocks until MCP initialization is complete.
+// If Initialize was never called, this returns immediately.
+func WaitForInit(ctx context.Context) error {
+	select {
+	case <-initDone:
+		return nil
+	case <-ctx.Done():
+		return ctx.Err()
+	}
 }
 
 func getOrRenewClient(ctx context.Context, name string) (*mcp.ClientSession, error) {