diff --git a/internal/api/server_config.go b/internal/api/server_config.go
index 275d837..6d78f7d 100644
--- a/internal/api/server_config.go
+++ b/internal/api/server_config.go
@@ -3,7 +3,6 @@ package api
 import (
 	"fmt"
 	"log"
-	"os"
 	"path/filepath"
 	"strings"
 
@@ -135,15 +134,20 @@ func secureFileRead(path string) ([]byte, error) {
 	return fileutil.SecureFileRead(path)
 }
 
-// EnsureLogDirectory creates the log directory if needed
+// EnsureLogDirectory creates the log directory if needed using PathRegistry
 func (c *ServerConfig) EnsureLogDirectory() error {
 	if c.Logging.File == "" {
 		return nil
 	}
 
-	logDir := filepath.Dir(c.Logging.File)
-	log.Printf("Creating log directory: %s", logDir)
-	return os.MkdirAll(logDir, 0750)
+	// Use PathRegistry for consistent log directory management
+	paths := config.FromEnv()
+	logDir := paths.LogDir()
+
+	if err := paths.EnsureDir(logDir); err != nil {
+		return fmt.Errorf("failed to create log directory: %w", err)
+	}
+	return nil
 }
 
 // BuildAuthConfig creates the auth configuration
@@ -163,11 +167,14 @@ func (c *ServerConfig) Validate() error {
 		c.Server.Address = ":8080"
 	}
 
+	// Use PathRegistry for consistent path management
+	paths := config.FromEnv()
+
 	if c.BasePath == "" {
-		c.BasePath = "/tmp/ml-experiments"
+		c.BasePath = paths.ExperimentsDir()
 	}
 	if c.DataDir == "" {
-		c.DataDir = config.DefaultDataDir
+		c.DataDir = paths.DataDir()
 	}
 
 	backend := strings.ToLower(strings.TrimSpace(c.Queue.Backend))