diff --git a/internal/detector/mcp.go b/internal/detector/mcp.go
index a7379ca..471277d 100644
--- a/internal/detector/mcp.go
+++ b/internal/detector/mcp.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"encoding/base64"
 	"encoding/json"
+	"path/filepath"
 	"strings"
 
 	"github.com/step-security/dev-machine-guard/internal/executor"
@@ -58,6 +59,15 @@ func (d *MCPDetector) Detect(_ context.Context, userIdentity string, enterprise
 		})
 	}
 
+	// Discover project-level .mcp.json files from known project paths
+	for _, projectMCP := range d.discoverProjectMCPConfigs(homeDir) {
+		results = append(results, model.MCPConfig{
+			ConfigSource: projectMCP.SourceName,
+			ConfigPath:   projectMCP.ConfigPath,
+			Vendor:       projectMCP.Vendor,
+		})
+	}
+
 	return results
 }
 
@@ -90,9 +100,68 @@ func (d *MCPDetector) DetectEnterprise(_ context.Context) []model.MCPConfigEnter
 		})
 	}
 
+	// Discover project-level .mcp.json files from known project paths
+	for _, projectMCP := range d.discoverProjectMCPConfigs(homeDir) {
+		content, err := d.exec.ReadFile(projectMCP.ConfigPath)
+		if err != nil || len(content) == 0 {
+			continue
+		}
+
+		filteredContent := d.filterMCPContent(projectMCP.SourceName, projectMCP.ConfigPath, content)
+		contentBase64 := base64.StdEncoding.EncodeToString(filteredContent)
+
+		results = append(results, model.MCPConfigEnterprise{
+			ConfigSource:        projectMCP.SourceName,
+			ConfigPath:          projectMCP.ConfigPath,
+			Vendor:              projectMCP.Vendor,
+			ConfigContentBase64: contentBase64,
+		})
+	}
+
 	return results
 }
 
+// discoverProjectMCPConfigs finds project-level .mcp.json files by reading project paths
+// from ~/.claude.json's "projects" section.
+func (d *MCPDetector) discoverProjectMCPConfigs(homeDir string) []mcpConfigSpec {
+	claudeJSONPath := expandTilde("~/.claude.json", homeDir)
+
+	content, err := d.exec.ReadFile(claudeJSONPath)
+	if err != nil || len(content) == 0 {
+		return nil
+	}
+
+	var parsed struct {
+		Projects map[string]json.RawMessage `json:"projects"`
+	}
+	if err := json.Unmarshal(content, &parsed); err != nil || len(parsed.Projects) == 0 {
+		return nil
+	}
+
+	var specs []mcpConfigSpec
+	seen := make(map[string]bool)
+
+	for projectPath := range parsed.Projects {
+		mcpPath := filepath.Join(projectPath, ".mcp.json")
+		if seen[mcpPath] {
+			continue
+		}
+		seen[mcpPath] = true
+
+		if !d.exec.FileExists(mcpPath) {
+			continue
+		}
+
+		specs = append(specs, mcpConfigSpec{
+			SourceName: "project_mcp",
+			ConfigPath: mcpPath,
+			Vendor:     "Project",
+		})
+	}
+
+	return specs
+}
+
 // resolveConfigPath returns the appropriate config path for the current platform.
 func (d *MCPDetector) resolveConfigPath(spec mcpConfigSpec, homeDir string) string {
 	if d.exec.GOOS() == "windows" && spec.WinConfigPath != "" {
@@ -131,17 +200,67 @@ func (d *MCPDetector) filterMCPContent(sourceName, configPath string, content []
 	return out
 }
 
-// extractMCPServers extracts mcpServers/context_servers, keeping only command/args/serverUrl/url.
+// extractMCPServers extracts mcpServers/context_servers/servers, keeping only command/args/serverUrl/url.
+// Also handles Claude Code's project-scoped mcpServers nested under projects → <path> → mcpServers.
 func (d *MCPDetector) extractMCPServers(raw map[string]json.RawMessage) map[string]any {
-	// Try mcpServers
+	result := make(map[string]any)
+	found := false
+
+	// Try mcpServers (Cursor, Claude Desktop)
 	if servers, ok := raw["mcpServers"]; ok {
-		return map[string]any{"mcpServers": filterServerFields(servers)}
+		result["mcpServers"] = filterServerFields(servers)
+		found = true
 	}
-	// Try context_servers
+	// Try context_servers (Zed)
 	if servers, ok := raw["context_servers"]; ok {
-		return map[string]any{"context_servers": filterServerFields(servers)}
+		result["context_servers"] = filterServerFields(servers)
+		found = true
+	}
+	// Try servers (VS Code mcp.json)
+	if servers, ok := raw["servers"]; ok {
+		result["servers"] = filterServerFields(servers)
+		found = true
+	}
+	// Try project-scoped mcpServers (Claude Code ~/.claude.json)
+	// Structure: { "projects": { "<path>": { "mcpServers": { ... } } } }
+	if projectsRaw, ok := raw["projects"]; ok {
+		filteredProjects := filterProjectScopedMCPServers(projectsRaw)
+		if filteredProjects != nil {
+			result["projects"] = filteredProjects
+			found = true
+		}
+	}
+
+	if !found {
+		return nil
+	}
+	return result
+}
+
+// filterProjectScopedMCPServers extracts mcpServers from each project in the projects map.
+// Returns only projects that have mcpServers, with server fields filtered.
+func filterProjectScopedMCPServers(projectsRaw json.RawMessage) map[string]any {
+	var projects map[string]map[string]json.RawMessage
+	if err := json.Unmarshal(projectsRaw, &projects); err != nil {
+		return nil
+	}
+
+	filtered := make(map[string]any)
+	for path, projectConfig := range projects {
+		serversRaw, ok := projectConfig["mcpServers"]
+		if !ok {
+			continue
+		}
+		serverFields := filterServerFields(serversRaw)
+		if len(serverFields) > 0 {
+			filtered[path] = map[string]any{"mcpServers": serverFields}
+		}
+	}
+
+	if len(filtered) == 0 {
+		return nil
 	}
-	return nil
+	return filtered
 }
 
 // filterServerFields keeps only command, args, serverUrl, url from each server entry.
diff --git a/internal/detector/mcp_test.go b/internal/detector/mcp_test.go
index f3380b9..2a64059 100644
--- a/internal/detector/mcp_test.go
+++ b/internal/detector/mcp_test.go
@@ -2,6 +2,7 @@ package detector
 
 import (
 	"context"
+	"encoding/json"
 	"testing"
 
 	"github.com/step-security/dev-machine-guard/internal/executor"
@@ -82,6 +83,162 @@ func TestMCPDetector_Enterprise(t *testing.T) {
 	}
 }
 
+func TestExtractMCPServers_ClaudeCodeProjectScoped(t *testing.T) {
+	det := &MCPDetector{}
+
+	// Claude Code ~/.claude.json with project-scoped mcpServers
+	content := []byte(`{
+		"numStartups": 10,
+		"projects": {
+			"/Users/test/project-a": {
+				"allowedTools": [],
+				"mcpServers": {
+					"notion": {"url": "https://mcp.notion.com/mcp", "headers": {"secret": "redacted"}}
+				}
+			},
+			"/Users/test/project-b": {
+				"allowedTools": [],
+				"mcpServers": {
+					"linear": {"url": "https://mcp.linear.app/mcp"}
+				}
+			},
+			"/Users/test/project-c": {
+				"allowedTools": []
+			}
+		}
+	}`)
+
+	filtered := det.filterMCPContent("claude_code", "/Users/test/.claude.json", content)
+
+	// Parse the result to verify structure
+	var result map[string]any
+	if err := json.Unmarshal(filtered, &result); err != nil {
+		t.Fatalf("failed to parse filtered content: %v", err)
+	}
+
+	// Should have projects key
+	projects, ok := result["projects"].(map[string]any)
+	if !ok {
+		t.Fatal("expected projects key in filtered output")
+	}
+
+	// Should only have projects with mcpServers (project-c should be excluded)
+	if len(projects) != 2 {
+		t.Errorf("expected 2 projects with mcpServers, got %d", len(projects))
+	}
+
+	// Should not have non-MCP fields like numStartups
+	if _, ok := result["numStartups"]; ok {
+		t.Error("non-MCP field numStartups should be filtered out")
+	}
+
+	// Verify server fields are filtered (no headers/secret)
+	projA, ok := projects["/Users/test/project-a"].(map[string]any)
+	if !ok {
+		t.Fatal("expected project-a in output")
+	}
+	mcpServers, ok := projA["mcpServers"].(map[string]any)
+	if !ok {
+		t.Fatal("expected mcpServers in project-a")
+	}
+	notion, ok := mcpServers["notion"].(map[string]any)
+	if !ok {
+		t.Fatal("expected notion server in project-a")
+	}
+	if _, ok := notion["headers"]; ok {
+		t.Error("headers should be filtered out from server config")
+	}
+	if notion["url"] != "https://mcp.notion.com/mcp" {
+		t.Errorf("expected notion url, got %v", notion["url"])
+	}
+}
+
+func TestExtractMCPServers_VSCodeFormat(t *testing.T) {
+	det := &MCPDetector{}
+
+	content := []byte(`{
+		"servers": {
+			"my-server": {"command": "npx", "args": ["-y", "server"], "env": {"SECRET": "key"}}
+		}
+	}`)
+
+	filtered := det.filterMCPContent("vscode", "/Users/test/.vscode/mcp.json", content)
+
+	var result map[string]any
+	if err := json.Unmarshal(filtered, &result); err != nil {
+		t.Fatalf("failed to parse filtered content: %v", err)
+	}
+
+	servers, ok := result["servers"].(map[string]any)
+	if !ok {
+		t.Fatal("expected servers key in filtered output")
+	}
+
+	srv, ok := servers["my-server"].(map[string]any)
+	if !ok {
+		t.Fatal("expected my-server in output")
+	}
+	if srv["command"] != "npx" {
+		t.Errorf("expected command npx, got %v", srv["command"])
+	}
+	if _, ok := srv["env"]; ok {
+		t.Error("env should be filtered out")
+	}
+}
+
+func TestMCPDetector_DiscoverProjectMCPConfigs(t *testing.T) {
+	mock := executor.NewMock()
+
+	// Set up ~/.claude.json with project paths
+	claudeJSON := `{
+		"projects": {
+			"/Users/testuser/project-a": {"allowedTools": []},
+			"/Users/testuser/project-b": {"allowedTools": []},
+			"/Users/testuser/project-c": {"allowedTools": []}
+		}
+	}`
+	mock.SetFile("/Users/testuser/.claude.json", []byte(claudeJSON))
+
+	// Only project-a and project-b have .mcp.json files
+	mock.SetFile("/Users/testuser/project-a/.mcp.json",
+		[]byte(`{"mcpServers":{"notion":{"url":"https://mcp.notion.com/mcp"}}}`))
+	mock.SetFile("/Users/testuser/project-b/.mcp.json",
+		[]byte(`{"mcpServers":{"linear":{"url":"https://mcp.linear.app/mcp"}}}`))
+
+	det := NewMCPDetector(mock)
+	results := det.DetectEnterprise(context.Background())
+
+	// Should find: claude.json (global) + 2 project-level .mcp.json
+	projectMCPCount := 0
+	for _, r := range results {
+		if r.ConfigSource == "project_mcp" {
+			projectMCPCount++
+		}
+	}
+
+	if projectMCPCount != 2 {
+		t.Errorf("expected 2 project-level MCP configs, got %d", projectMCPCount)
+	}
+
+	// Verify project paths
+	foundA := false
+	foundB := false
+	for _, r := range results {
+		if r.ConfigPath == "/Users/testuser/project-a/.mcp.json" {
+			foundA = true
+		}
+		if r.ConfigPath == "/Users/testuser/project-b/.mcp.json" {
+			foundB = true
+		}
+	}
+	if !foundA {
+		t.Error("expected project-a .mcp.json to be found")
+	}
+	if !foundB {
+		t.Error("expected project-b .mcp.json to be found")
+	}
+}
+
 func TestMCPDetector_Windows_FindsConfigs(t *testing.T) {
 	mock := executor.NewMock()
 	mock.SetGOOS("windows")