Preheat the oven to 375 degrees. Line a baking sheet with foil or parchment paper.
Heat the olive oil in a large skillet over medium heat. Add the ground beef and break the meat into crumbles. Add the onion as well as the seasonings then cook for 4-5 minutes, stirring occasionally, until the meat is cooked through and the onion is tender.
Add the minced garlic and cook, stirring constantly, for 1 minute. Remove the beef mixture from the stove and set it aside to cool.
Wrap flour tortillas in wet paper towels and microwave them for 1 minute or until soft.
Place some refried beans down the center of the tortilla followed by a sprinkling of pepper Jack cheese then top with some of the ground beef mixture; roll.
Place, seam side down, on a baking sheet that's been coated with cooking spray. Finish rolling the rest of the flautas, then spray each of them well with cooking spray.
Place into the oven and bake for 8-10 minutes then turn over and cook for an additional 5-6 minutes or until crispy and golden brown.
Serve the flautas with a side of guacamole, sour cream, and/or salsa for dipping. Enjoy.