First, preheat oven to 350ºF. Then generously spray a muffin tin with nonstick cooking spray and set aside.
Heat olive oil in a large nonstick pan over medium/high heat. When olive oil is fragrant, add yellow onion. Saute for around 3 minutes. Then, add mushrooms and garlic and saute for another 3 minutes. Then add asparagus and saute for another 3 minutes.
While the veggies are cooking, whisk together eggs, milk, salt, and pepper. Set aside.
After the veggies have been cooked, spoon in around 1-2 tablespoons of veggies into each muffin. You should fill each cup around 1/2 full.
Next, fill each muffin with the egg mixture around 2/3 of the way full. Then, separate out around 1/4 cup of shredded cheese.
Bake at 350ºF for 15 minutes. Remove from oven, sprinkle on the remaining shredded cheese and bake for another 2-3 minutes.