Heat the butter in a large skillet over medium heat. Add the onion, jalapeños, garlic, cumin, and a pinch of salt. Cook until the onion is fragrant, about 5-10 minutes. Add the cream cheese and milk. Cook over medium heat until the sauce is smooth and the cream cheese has melted.
In a bowl, toss together the shredded cheese with the flour. Little by little, add the cheese to the warm milk, whisking until the sauce is smooth. Stir in the chipotle peppers.
Serve the queso warm topped with salsa and avocado. Use chips for scooping.
