diff --git a/internal/runtime/executor/claude_executor.go b/internal/runtime/executor/claude_executor.go
index ff045c51..e6cabde3 100644
--- a/internal/runtime/executor/claude_executor.go
+++ b/internal/runtime/executor/claude_executor.go
@@ -753,17 +753,11 @@ func applyClaudeToolPrefix(body []byte, prefix string) []byte {
 		return body
 	}
 
-	// Build a set of built-in tool names (tools with a "type" field)
-	builtinTools := make(map[string]bool)
-	if tools := gjson.GetBytes(body, "tools"); tools.Exists() && tools.IsArray() {
-		tools.ForEach(func(_, tool gjson.Result) bool {
-			if tool.Get("type").Exists() && tool.Get("type").String() != "" {
-				if name := tool.Get("name").String(); name != "" {
-					builtinTools[name] = true
-				}
-			}
-			return true
-		})
+	// Collect built-in tool names (those with a non-empty "type" field) so we can
+	// skip them consistently in both tools and message history.
+	builtinTools := map[string]bool{}
+	for _, name := range []string{"web_search", "code_execution", "text_editor", "computer"} {
+		builtinTools[name] = true
 	}
 
 	if tools := gjson.GetBytes(body, "tools"); tools.Exists() && tools.IsArray() {
@@ -771,6 +765,9 @@ func applyClaudeToolPrefix(body []byte, prefix string) []byte {
 			// Skip built-in tools (web_search, code_execution, etc.) which have
 			// a "type" field and require their name to remain unchanged.
 			if tool.Get("type").Exists() && tool.Get("type").String() != "" {
+				if n := tool.Get("name").String(); n != "" {
+					builtinTools[n] = true
+				}
 				return true
 			}
 			name := tool.Get("name").String()
@@ -785,7 +782,7 @@ func applyClaudeToolPrefix(body []byte, prefix string) []byte {
 
 	if gjson.GetBytes(body, "tool_choice.type").String() == "tool" {
 		name := gjson.GetBytes(body, "tool_choice.name").String()
-		if name != "" && !strings.HasPrefix(name, prefix) {
+		if name != "" && !strings.HasPrefix(name, prefix) && !builtinTools[name] {
 			body, _ = sjson.SetBytes(body, "tool_choice.name", prefix+name)
 		}
 	}
@@ -801,7 +798,7 @@ func applyClaudeToolPrefix(body []byte, prefix string) []byte {
 				switch partType {
 				case "tool_use":
 					name := part.Get("name").String()
-					if name == "" || strings.HasPrefix(name, prefix) {
+					if name == "" || strings.HasPrefix(name, prefix) || builtinTools[name] {
 						return true
 					}
 					path := fmt.Sprintf("messages.%d.content.%d.name", msgIndex.Int(), contentIndex.Int())
diff --git a/internal/runtime/executor/claude_executor_test.go b/internal/runtime/executor/claude_executor_test.go
index 18594146..017e0913 100644
--- a/internal/runtime/executor/claude_executor_test.go
+++ b/internal/runtime/executor/claude_executor_test.go
@@ -49,6 +49,97 @@ func TestApplyClaudeToolPrefix_SkipsBuiltinTools(t *testing.T) {
 	}
 }
 
+func TestApplyClaudeToolPrefix_BuiltinToolSkipped(t *testing.T) {
+	body := []byte(`{
+		"tools": [
+			{"type": "web_search_20250305", "name": "web_search", "max_uses": 5},
+			{"name": "Read"}
+		],
+		"messages": [
+			{"role": "user", "content": [
+				{"type": "tool_use", "name": "web_search", "id": "ws1", "input": {}},
+				{"type": "tool_use", "name": "Read", "id": "r1", "input": {}}
+			]}
+		]
+	}`)
+	out := applyClaudeToolPrefix(body, "proxy_")
+
+	if got := gjson.GetBytes(out, "tools.0.name").String(); got != "web_search" {
+		t.Fatalf("tools.0.name = %q, want %q", got, "web_search")
+	}
+	if got := gjson.GetBytes(out, "messages.0.content.0.name").String(); got != "web_search" {
+		t.Fatalf("messages.0.content.0.name = %q, want %q", got, "web_search")
+	}
+	if got := gjson.GetBytes(out, "tools.1.name").String(); got != "proxy_Read" {
+		t.Fatalf("tools.1.name = %q, want %q", got, "proxy_Read")
+	}
+	if got := gjson.GetBytes(out, "messages.0.content.1.name").String(); got != "proxy_Read" {
+		t.Fatalf("messages.0.content.1.name = %q, want %q", got, "proxy_Read")
+	}
+}
+
+func TestApplyClaudeToolPrefix_KnownBuiltinInHistoryOnly(t *testing.T) {
+	body := []byte(`{
+		"tools": [
+			{"name": "Read"}
+		],
+		"messages": [
+			{"role": "user", "content": [
+				{"type": "tool_use", "name": "web_search", "id": "ws1", "input": {}}
+			]}
+		]
+	}`)
+	out := applyClaudeToolPrefix(body, "proxy_")
+
+	if got := gjson.GetBytes(out, "messages.0.content.0.name").String(); got != "web_search" {
+		t.Fatalf("messages.0.content.0.name = %q, want %q", got, "web_search")
+	}
+	if got := gjson.GetBytes(out, "tools.0.name").String(); got != "proxy_Read" {
+		t.Fatalf("tools.0.name = %q, want %q", got, "proxy_Read")
+	}
+}
+
+func TestApplyClaudeToolPrefix_CustomToolsPrefixed(t *testing.T) {
+	body := []byte(`{
+		"tools": [{"name": "Read"}, {"name": "Write"}],
+		"messages": [
+			{"role": "user", "content": [
+				{"type": "tool_use", "name": "Read", "id": "r1", "input": {}},
+				{"type": "tool_use", "name": "Write", "id": "w1", "input": {}}
+			]}
+		]
+	}`)
+	out := applyClaudeToolPrefix(body, "proxy_")
+
+	if got := gjson.GetBytes(out, "tools.0.name").String(); got != "proxy_Read" {
+		t.Fatalf("tools.0.name = %q, want %q", got, "proxy_Read")
+	}
+	if got := gjson.GetBytes(out, "tools.1.name").String(); got != "proxy_Write" {
+		t.Fatalf("tools.1.name = %q, want %q", got, "proxy_Write")
+	}
+	if got := gjson.GetBytes(out, "messages.0.content.0.name").String(); got != "proxy_Read" {
+		t.Fatalf("messages.0.content.0.name = %q, want %q", got, "proxy_Read")
+	}
+	if got := gjson.GetBytes(out, "messages.0.content.1.name").String(); got != "proxy_Write" {
+		t.Fatalf("messages.0.content.1.name = %q, want %q", got, "proxy_Write")
+	}
+}
+
+func TestApplyClaudeToolPrefix_ToolChoiceBuiltin(t *testing.T) {
+	body := []byte(`{
+		"tools": [
+			{"type": "web_search_20250305", "name": "web_search"},
+			{"name": "Read"}
+		],
+		"tool_choice": {"type": "tool", "name": "web_search"}
+	}`)
+	out := applyClaudeToolPrefix(body, "proxy_")
+
+	if got := gjson.GetBytes(out, "tool_choice.name").String(); got != "web_search" {
+		t.Fatalf("tool_choice.name = %q, want %q", got, "web_search")
+	}
+}
+
 func TestStripClaudeToolPrefixFromResponse(t *testing.T) {
 	input := []byte(`{"content":[{"type":"tool_use","name":"proxy_alpha","id":"t1","input":{}},{"type":"tool_use","name":"bravo","id":"t2","input":{}}]}`)
 	out := stripClaudeToolPrefixFromResponse(input, "proxy_")