Melt butter in a small pot over medium heat. Add chopped onion and cook until translucent. Add in flour, garlic powder, and chipotle pepper and stir until butter is absorbed into the flour. Add 1/3 cup of milk and stir until incorporated. Add the remaining milk and stirring occasionally until completely incorporated and thickened (about 5 minutes)

Stir in the nutritional yeast and salt, tasting and adjusting as necessary. Serve immediately with your chips! To store in the fridge, use plastic wrap against the surface of the remaining dip to prevent a skin from forming.