In a large skillet over medium-high heat, brown the sausage. Add in the pepper and onion until they are tender (5-7 minutes).
In a separate bowl, beat together eggs and milk.
Reduce heat to medium, then add in eggs. Stir and scrape the entire mixture until eggs are completely scrambled.
Place a flour tortilla on heated griddle, sprinkle on 1/3 cup cheese and 1/3 of the egg mixture, with a second tortilla on top. Cook for 3 to 5 minutes, or until tortilla is golden brown, turning over halfway through. Repeat two times.
Notes
You can also use a quesadilla maker (they're super easy to use and quickly make quesadillas).