diff --git a/src/main.c b/src/main.c
index df78133..7c07d54 100644
--- a/src/main.c
+++ b/src/main.c
@@ -3052,12 +3052,7 @@ int main(int argc, char* argv[]) {
                     log_error("Invalid port number");
                     return 1;
                 }
-                // Store port in configuration system
-                char port_str[16];
-                snprintf(port_str, sizeof(port_str), "%d", port);
-                set_database_config("relay_port", port_str, "command_line");
-                // Re-apply configuration to make sure global variables are updated
-                apply_configuration_to_globals();
+                // Port will be stored in configuration system after it's initialized
             } else {
                 log_error("Port argument requires a value");
                 return 1;
@@ -3141,6 +3136,17 @@ int main(int argc, char* argv[]) {
         return 1;
     }
     
+    // Apply command line overrides AFTER configuration system is initialized
+    if (port != DEFAULT_PORT) {
+        log_info("Applying port override from command line");
+        printf("  Port: %d\n", port);
+        char port_str[16];
+        snprintf(port_str, sizeof(port_str), "%d", port);
+        if (set_database_config("relay_port", port_str, "command_line") != 0) {
+            log_warning("Failed to set port override in configuration");
+        }
+    }
+    
     // Initialize NIP-11 relay information
     init_relay_info();
     
diff --git a/test_combined.db b/test_combined.db
new file mode 100644
index 0000000..b6477f1
Binary files /dev/null and b/test_combined.db differ