Cook the chorizo in a skillet over medium heat until crumbled and evenly browned, about 5 minutes; drain and set aside. Cook the onion in the same skillet until soft; stir in the eggs and scramble with the onion. Mix in the tomatoes and continue to cook and stir until eggs are nearly set; remove from heat.
Spread a layer of tortilla chips into a 9×13 baking dish. Scatter the chorizo and the scrambled egg mixture over the chips. Top with jalapeno slices and cover with the cheese.
Bake in preheated oven until cheese is melted, 7 to 10 minutes.