In a medium saucepan over medium heat, melt the butter. Add the chopped yellow onion and sauté for about 3-4 minutes until it becomes translucent. Next, add the seeded and chopped jalapeños along with the minced garlic. Cook for an additional 2 minutes until fragrant.
Sprinkle in the cumin and salt, stirring well to combine. This will create a flavorful base for your queso.
Reduce the heat to low and add the cream cheese to the saucepan, stirring continuously until melted and combined with the onion mixture.
Slowly pour in the whole milk while stirring. This will help create a smooth and creamy consistency for your queso.
Sprinkle the all-purpose flour over the mixture, stirring constantly to prevent lumps. Continue to cook and stir for about 2-3 minutes until the mixture begins to thicken.
Gradually add the shredded sharp cheddar and Monterey Jack cheese, stirring until melted and smooth.
Stir in the finely minced chipotle peppers in adobo for a smoky kick. Adjust the amount to suit your heat preference.
Remove from heat and serve immediately with mango salsa, red salsa, sliced avocado, and a generous amount of tortilla chips for dipping.