diff --git a/pkg/tools/registry.go b/pkg/tools/registry.go
index f8f0aa3fd..e90d683bb 100644
--- a/pkg/tools/registry.go
+++ b/pkg/tools/registry.go
@@ -172,6 +172,13 @@ func (r *ToolRegistry) toolAllowedLocked(name string) bool {
 	if r.allowlist == nil {
 		return true
 	}
+	if isToolDiscoveryToolName(name) {
+		// Discovery tools are part of the MCP control plane: they must remain
+		// available whenever configured so deferred MCP tools can still be
+		// unlocked. Per-agent allowlists still apply to the hidden MCP tools
+		// themselves during RegisterHidden.
+		return true
+	}
 	_, ok := r.allowlist[strings.ToLower(strings.TrimSpace(name))]
 	return ok
 }
diff --git a/pkg/tools/registry_test.go b/pkg/tools/registry_test.go
index f75a321f2..ee63586ab 100644
--- a/pkg/tools/registry_test.go
+++ b/pkg/tools/registry_test.go
@@ -130,6 +130,25 @@ func TestToolRegistry_AllowlistFiltersRegistrations(t *testing.T) {
 	}
 }
 
+func TestToolRegistry_AllowlistStillAllowsDiscoveryTools(t *testing.T) {
+	r := NewToolRegistry()
+	r.SetAllowlist([]string{"mcp_github_search"})
+
+	r.Register(newMockTool(BM25SearchToolName, "discover hidden tools"))
+	r.Register(newMockTool(RegexSearchToolName, "discover hidden tools via regex"))
+	r.Register(newMockTool("blocked_tool", "blocked"))
+
+	if _, ok := r.Get(BM25SearchToolName); !ok {
+		t.Fatal("expected BM25 discovery tool to bypass allowlist filtering")
+	}
+	if _, ok := r.Get(RegexSearchToolName); !ok {
+		t.Fatal("expected regex discovery tool to bypass allowlist filtering")
+	}
+	if _, ok := r.Get("blocked_tool"); ok {
+		t.Fatal("blocked_tool should not be registered")
+	}
+}
+
 func TestToolRegistry_HasRegisteredIncludesHiddenTools(t *testing.T) {
 	r := NewToolRegistry()
 	r.SetAllowlist([]string{"visible", "hidden"})
diff --git a/pkg/tools/search_tool.go b/pkg/tools/search_tool.go
index c5884c9de..511b81a03 100644
--- a/pkg/tools/search_tool.go
+++ b/pkg/tools/search_tool.go
@@ -14,6 +14,8 @@ import (
 
 const (
 	MaxRegexPatternLength = 200
+	RegexSearchToolName   = "tool_search_tool_regex"
+	BM25SearchToolName    = "tool_search_tool_bm25"
 )
 
 type RegexSearchTool struct {
@@ -27,7 +29,7 @@ func NewRegexSearchTool(r *ToolRegistry, ttl int, maxSearchResults int) *RegexSe
 }
 
 func (t *RegexSearchTool) Name() string {
-	return "tool_search_tool_regex"
+	return RegexSearchToolName
 }
 
 func (t *RegexSearchTool) Description() string {
@@ -96,7 +98,7 @@ func NewBM25SearchTool(r *ToolRegistry, ttl int, maxSearchResults int) *BM25Sear
 }
 
 func (t *BM25SearchTool) Name() string {
-	return "tool_search_tool_bm25"
+	return BM25SearchToolName
 }
 
 func (t *BM25SearchTool) Description() string {
@@ -294,6 +296,15 @@ func (t *BM25SearchTool) getOrBuildEngine() *bm25CachedEngine {
 	return cached
 }
 
+func isToolDiscoveryToolName(name string) bool {
+	switch strings.ToLower(strings.TrimSpace(name)) {
+	case BM25SearchToolName, RegexSearchToolName:
+		return true
+	default:
+		return false
+	}
+}
+
 // SearchBM25 ranks hidden tools against query using BM25 via utils.BM25Engine.
 // This non-cached variant rebuilds the engine on every call. Used by tests
 // and any code that doesn't hold a BM25SearchTool instance.