Chili Cheese Manicotti are large pasta tubes surrounded and stuffed with a flavorful cheesy beef mixture that definitely has a kick! I got the idea after craving (and eating a few) chili cheese burritos at Taco Bell. If you like a little spice in your recipes, be sure to try my Spicy Steak Chili. For a couple of chili cheese appetizers, try my Chili Cheese Fries and Chili Cheese Nachos.

Three Chili Cheese Manicotti's on a White Plate

Chili Cheese Manicotti

It makes sense that manicotti means ‘little sleeve’. This pasta is intended to be stuffed and baked. Chili Cheese Manicotti definitely takes full advantage of all the flavor that can be stuffed into each ‘little sleeve’. Plus, there is enough of the chili and beef mixture to add a layer above and below the manicotti, bringing out even more of the chili flavor!

Chili Cheese Manicotti in a White Casserole Dish

Chili Cheese Manicotti Recipe

It’s all about the spices and cheese that bring so much flavor to the Chili Cheese Manicotti. So, get out a pot and a large skillet and make sure you have all the ingredients on hand to make this spicy dish.

Chili Cheese Manicotti Being Lifted Out of Pan on Spatula

How to Make Chili Cheese Manicotti

One important part about this recipe is cooking the manicotti noodles al dente. You want them sturdy enough to hold the filling. Let them cool a bit before you fill them. While they are cooking and cooling, prepare the chili cheese mixture.

  1. In a large skillet, brown the ground beef with the onion.
  2. Add in all the seasonings from the chili powder to the pepper.
  3. Pour in the water and make sure all the seasonings are well mixed in and dissolved.
  4. In a separate small bowl, combine and mix the corn starch with 2 tablespoons water. Pour it in the skillet.
  5. Add the refried beans, chili beans, and tomato paste. Continue stirring until everything is combined and smooth.
  6. Fold in 2 cups of the shredded cheese until it is completely melted.
  7. Reduce heat to medium-low and let it simmer for about 10 minutes, stirring it occasionally so it doesn’t stick.

Assembling the Chili Cheese Manicotti

After you have the chili cheese mixture ready, it’s time to fill the noodles and bake them. First, put a layer of the chili cheese sauce down on the bottom of a 9×13-inch baking pan. Then, fill each noodle, placing them in the pan after filling. To fill the noodles, pinch one end closed while you spoon in the mixture to fill up the noodle. After all the noodles are filled, top them off with the remaining chili cheese sauce and shredded cheddar cheese. Finally, bake the Chili Cheese Manicotti for 15-20 minutes at 350°F. Top with sour cream and onion.

Cut into Chili Cheese Manicotti

More Stuffed Shells Recipes

5 from 1 vote

Chili Cheese Manicotti

Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Stuffed and layered with a chili cheese sauce makes this Chili Cheese Manicotti really stand out!


  • 1 box manicotti shells, cooked al dente and drained
  • 1 pound ground beef
  • 1 yellow onion, diced
  • 2 tablespoons chili powder
  • 2 teaspoons ground cumin
  • ½ teaspoon cayenne pepper
  • ½ teaspoon garlic powder
  • 1 teaspoon onion powder
  • 2 teaspoons salt
  • ½ teaspoon pepper
  • 1 cup water
  • 2 tablespoons corn starch, combined with 2 tablespoons water
  • 1 can refried beans
  • 1 can chili beans
  • 1 can tomato paste
  • 2 ½ cups sharp cheddar cheese, shredded and divided
  • ¼ cup onion, diced for topping
  • ¼ cup sour cream, for topping


  • Preheat oven to 350°F.
  • In a large skillet, over medium heat, brown the ground beef along with the diced onion.
  • Add the chili powder, ground cumin, cayenne pepper, garlic powder, onion powder, salt, and pepper to the ground beef.
  • Pour in the water and make sure the seasoning is well mixed in and dissolved.
  • In a small bowl, combine the corn starch and 2 tablespoons water. Add it to the skillet.
  • Add the refried beans, chili beans, and tomato paste to the skillet. Keep stirring until the refried beans and tomato paste have become smooth and everything is well combined.
  • Slowly add 2 cups of the shredded cheese to the skillet. Keep folding in the cheese until it has all melted.
  • Reduce heat to medium-low. Let the mixture simmer for about 10 minutes, stirring frequently so nothing sticks and burns on the bottom.
  • Add one cup of the beef mixture to the bottom of a 9×13-inch baking dish.
  • Fill the cooked noodles with the mixture by holding one end of the noodle closed and stuffing the open end until filled. Place in the baking dish.
  • Top with any leftover mixture and the rest of the cheddar cheese.
  • Bake for 15-20 minutes, or until bubbly.
  • Top with sour cream and onion (optional).

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