Preheat the oven to 375 degrees. Line a baking sheet with foil or parchment paper and coat it with olive oil cooking spray.
Heat the olive oil in a large skillet over medium heat. Add the ground beef and break the meat into crumbles. Add the onion and 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 let it cool.
Wrap flour tortillas in a few wet paper towels. Microwave them for 30 to 60 seconds, or until soft.
Place some refried beans down the center of the tortilla. Top with Pepper Jack cheese, then some ground beef mixture, and roll.
Place the flauta, seam side down, on a baking sheet.
Brush each flauta with olive oil or coat with olive oil cooking spray.
Bake for 8-10 minutes.
Flip them over and cook for 5-7 minutes or until crispy and golden brown.