In a medium bowl, whisk together the eggs, whole milk, salt, and black pepper until fully combined.
Heat olive oil in a large non-stick skillet over medium heat. Add diced red bell pepper, green bell pepper, and yellow onion. Sauté for 4-5 minutes until vegetables are softened.
Pour the egg mixture into the skillet with the sautéed vegetables. Cook, stirring gently, until the eggs are fully set but still moist, about 4-5 minutes. Remove from heat.
Lay out the flour tortillas on a clean surface. Evenly distribute the cooked egg and vegetable mixture onto half of each tortilla.
Sprinkle shredded cheddar cheese evenly over the egg mixture on each tortilla.
Fold the tortillas in half to create quesadillas.
Heat a clean skillet over medium heat and lightly spray with cooking spray. Place one quesadilla in the skillet and cook for 2-3 minutes on each side until the tortilla is golden brown and the cheese is melted.
Remove from heat and let cool completely on a wire rack.
Once cooled, wrap each quesadilla tightly in plastic wrap and then in aluminum foil. Label and freeze for up to 2 months.
To reheat, unwrap the quesadilla and microwave on high for 1-2 minutes or until heated through, or reheat in a skillet over medium heat for 3-4 minutes per side.