diff --git a/pkg/providers/claude_cli_provider.go b/pkg/providers/claude_cli_provider.go
index 40b581490..9ce7004c9 100644
--- a/pkg/providers/claude_cli_provider.go
+++ b/pkg/providers/claude_cli_provider.go
@@ -27,13 +27,9 @@ func NewClaudeCliProvider(workspace string) *ClaudeCliProvider {
 func (p *ClaudeCliProvider) Chat(
 	ctx context.Context, messages []Message, tools []ToolDefinition, model string, options map[string]any,
 ) (*LLMResponse, error) {
-	systemPrompt := p.buildSystemPrompt(messages, tools)
-	prompt := p.messagesToPrompt(messages)
+	prompt := p.buildStdinPrompt(messages, tools)
 
 	args := []string{"-p", "--output-format", "json", "--dangerously-skip-permissions", "--no-chrome"}
-	if systemPrompt != "" {
-		args = append(args, "--system-prompt", systemPrompt)
-	}
 	if model != "" && model != "claude-code" {
 		args = append(args, "--model", model)
 	}
@@ -72,14 +68,26 @@ func (p *ClaudeCliProvider) GetDefaultModel() string {
 	return "claude-code"
 }
 
-// messagesToPrompt converts messages to a CLI-compatible prompt string.
+// buildStdinPrompt combines the system context and conversation into a single stdin payload.
+// Passing system instructions via stdin avoids exposing them in the process argument list and
+// sidesteps operating-system ARG_MAX limits when many tools are registered.
+func (p *ClaudeCliProvider) buildStdinPrompt(messages []Message, tools []ToolDefinition) string {
+	system := p.buildSystemPrompt(messages, tools)
+	conversation := p.messagesToPrompt(messages)
+	if system == "" {
+		return conversation
+	}
+	return system + "\n\n---\n\n" + conversation
+}
+
+// messagesToPrompt converts non-system messages to a CLI-compatible prompt string.
 func (p *ClaudeCliProvider) messagesToPrompt(messages []Message) string {
 	var parts []string
 
 	for _, msg := range messages {
 		switch msg.Role {
 		case "system":
-			// handled via --system-prompt flag
+			// included in system context block; see buildStdinPrompt
 		case "user":
 			parts = append(parts, "User: "+msg.Content)
 		case "assistant":
diff --git a/pkg/providers/claude_cli_provider_test.go b/pkg/providers/claude_cli_provider_test.go
index d4d648f5a..55e21da11 100644
--- a/pkg/providers/claude_cli_provider_test.go
+++ b/pkg/providers/claude_cli_provider_test.go
@@ -300,9 +300,27 @@ func TestChat_ContextCancellation(t *testing.T) {
 	}
 }
 
-func TestChat_PassesSystemPromptFlag(t *testing.T) {
-	argsFile := filepath.Join(t.TempDir(), "args.txt")
-	script := createArgCaptureCLI(t, argsFile)
+func TestChat_SystemPromptInStdinNotArgs(t *testing.T) {
+	if runtime.GOOS == "windows" {
+		t.Skip("mock CLI scripts not supported on Windows")
+	}
+
+	dir := t.TempDir()
+	argsFile := filepath.Join(dir, "args.txt")
+	stdinFile := filepath.Join(dir, "stdin.txt")
+
+	// Script captures both args and stdin content.
+	script := filepath.Join(dir, "claude")
+	scriptContent := fmt.Sprintf(`#!/bin/sh
+echo "$@" > '%s'
+cat - > '%s'
+cat <<'EOFMOCK'
+{"type":"result","result":"ok","session_id":"test"}
+EOFMOCK
+`, argsFile, stdinFile)
+	if err := os.WriteFile(script, []byte(scriptContent), 0o755); err != nil {
+		t.Fatal(err)
+	}
 
 	p := NewClaudeCliProvider(t.TempDir())
 	p.command = script
@@ -320,8 +338,20 @@ func TestChat_PassesSystemPromptFlag(t *testing.T) {
 		t.Fatalf("failed to read args file: %v", err)
 	}
 	args := string(argsBytes)
-	if !strings.Contains(args, "--system-prompt") {
-		t.Errorf("CLI args missing --system-prompt, got: %s", args)
+	if strings.Contains(args, "--system-prompt") {
+		t.Errorf("CLI args must not contain --system-prompt, got: %s", args)
+	}
+
+	stdinBytes, err := os.ReadFile(stdinFile)
+	if err != nil {
+		t.Fatalf("failed to read stdin file: %v", err)
+	}
+	stdin := string(stdinBytes)
+	if !strings.Contains(stdin, "Be helpful.") {
+		t.Errorf("stdin must contain system prompt content, got: %s", stdin)
+	}
+	if !strings.Contains(stdin, "Hi") {
+		t.Errorf("stdin must contain user message, got: %s", stdin)
 	}
 }
 
@@ -657,6 +687,36 @@ func TestBuildSystemPrompt_ToolsOnlyNoSystem(t *testing.T) {
 	}
 }
 
+// --- buildStdinPrompt tests ---
+
+func TestBuildStdinPrompt_NoSystem(t *testing.T) {
+	p := NewClaudeCliProvider("/workspace")
+	messages := []Message{{Role: "user", Content: "Hello"}}
+	got := p.buildStdinPrompt(messages, nil)
+	if got != "Hello" {
+		t.Errorf("buildStdinPrompt() without system = %q, want %q", got, "Hello")
+	}
+}
+
+func TestBuildStdinPrompt_WithSystem(t *testing.T) {
+	p := NewClaudeCliProvider("/workspace")
+	messages := []Message{
+		{Role: "system", Content: "Be concise."},
+		{Role: "user", Content: "Hello"},
+	}
+	got := p.buildStdinPrompt(messages, nil)
+	if !strings.Contains(got, "Be concise.") {
+		t.Error("buildStdinPrompt() must include system content")
+	}
+	if !strings.Contains(got, "Hello") {
+		t.Error("buildStdinPrompt() must include user content")
+	}
+	// System section must precede user section.
+	if strings.Index(got, "Be concise.") > strings.Index(got, "Hello") {
+		t.Error("buildStdinPrompt() system content must appear before user content")
+	}
+}
+
 // --- buildToolsPrompt tests ---
 
 func TestBuildToolsPrompt_SkipsNonFunction(t *testing.T) {
diff --git a/pkg/providers/gemini_cli_provider_test.go b/pkg/providers/gemini_cli_provider_test.go
index d513d8380..ddd22f2bc 100644
--- a/pkg/providers/gemini_cli_provider_test.go
+++ b/pkg/providers/gemini_cli_provider_test.go
@@ -261,6 +261,7 @@ func TestCreateProvider_GeminiCliWithModel(t *testing.T) {
 
 func TestCreateProvider_GeminiCliDefaultWorkspace(t *testing.T) {
 	cfg := config.DefaultConfig()
+	cfg.Agents.Defaults.Workspace = "" // clear default so the "." fallback is exercised
 	cfg.ModelList = []config.ModelConfig{
 		{ModelName: "gemini-cli", Model: "gemini-cli/gemini-cli"},
 	}