Preheat the oven to 400 degrees F (200 degrees C).
Cut squash into spirals using a spiralizer (fitted with the large shredding blade).
Combine squash, bell pepper, onion, and olive oil in a medium bowl; toss. Set aside.
Stir ricotta cheese and lemon zest together in a small bowl. Spread mixture evenly over naan, leaving a 1/2-inch border. Sprinkle Gruyere cheese over ricotta mixture. Add squash mixture, spreading evenly on naan. Sprinkle with red pepper flakes, salt, and pepper. Place on a baking sheet.
Bake in the preheated oven until bottom is crisp and edges are golden brown, about 12 minutes. Garnish with bail and serve with lemon wedges.