These chicken stuffed shells are filled with creamy cheese, rotisserie chicken, and bacon, then baked in a rich jalapeño cheese sauce. A comforting pasta bake inspired by jalapeño poppers and perfect for an easy weeknight dinner.

Chicken Stuffed Shells (Jalapeño Popper Pasta Bake with Bacon)

When it comes to guilty pleasures and comfort food, jalapeno popper anything is always at the top of my list!

What’s not to love about spicy jalapeno peppers paired up with a creamy, cheesy filling?

So it stands to reason if we add .. um .. bacon …. and maybe some shredded chicken that we would be on the path to taste bud nirvana.. right?

(..yes.. the answer is yes)

Over the top decadent cheesy pasta and the ultimate comfort food, these Jalapeno Popper Chicken Stuffed Shells have it all!

What Are Chicken Stuffed Shells?

So what exactly are Jalapeno Chicken Stuffed Shells?

Think of classic Italian stuffed shells but instead of those jumbo pasta shells being stuffed with ricotta cheese and covered in marinara sauce, we added a took a hard right.

This easy baked shells recipe combines classic stuffed shells and your favorite jalapeno popper appetizer.

We are taking those jumbo pasta shells and stuffing them with a creamy jalapeno popper mixture complete with bacon, jalapeno peppers and rotisserie chicken.

(… but WAIT! … there’s more!!)

And instead of marinara sauce, we are covering our stuffed shells with a creamy jalapeno cheese sauce, adding some shredded cheese and then baking them to perfection.

Healthy? .. no!

DELICIOUS baked shells recipe? … YES!!

Why This Chicken Stuffed Shell Recipe Works

New fun take on your classic stuffed shells recipe.
Combines the idea of Italian stuffed shells with your favorite jalapeno popper appetizer.
Spicy jalapeno peppers, creamy cheese sauce, rotisserie chicken and BACON!
Using rotisserie chicken is a quick, easy alternative to baking chicken at home.
The ultimate comfort food, this jalapeno popper pasta is the perfect weeknight dinner idea.
This jalapeno baked shells recipe yields a lot of shells, so it’s perfect for serving a crowd.
Leftovers are great for lunch or another quick dinner.

Ingredients for Chicken Stuffed Shells

Large jumbo pasta shells
Jalapeno peppers
Bacon
Cream cheese
Sour cream
Shredded cheddar cheese
Pepper Jack cheese
Rotisserie chicken
Green onions
Milk
Chicken stock
Butter
All purpose flour
Parmesan cheese
Spices

How to Make Chicken Stuffed Shells (Step-by-Step)

Start by preheating oven to 350 degrees and spraying a 9×13 baking pan with nonstick spray.
Bring a large pot of salted water to boil. Cook shells following box instructions but pull 1 minute early. Drain and set aside to cool slightly.
While pasta is cooking, make your jalapeno cheese sauce.

Jalapeño Popper Cheese Sauce (Creamy & Spicy)

Add diced jalapeno pepper to a large skillet and heat over medium high heat for 1-2 minutes. Add minced garlic and stir to cook for 1 minute.

Move 2/3 of the jalapeno and garlic to a large mixing bowl while leaving the remaining amount in your skillet.
To your skillet ,add in your butter and once your butter is melted, add in the flour.
Whisk together and continue whisking while your flour cooks for 1-2 minutes before slowly pouring in the milk and chicken stock.
Whisk together to combine and break up any flour clumps.
Add in salt and pepper and bring to a low boil, stirring often.
Once boiling, turn heat down to medium and stir in the Parmesan cheese and Pepper Jack cheese and continue to stir until all of your cheese has melted.

In a large bowl, combine bacon, 2 diced jalapeno peppers, shredded rotisserie chicken, cream cheese, sour cream, green onions, seasonings and 1/2 cup shredded cheese.

Spoon jalapeno popper mixture into the shells and place open sides up in the baking pan.

Cover with jalapeno cheese sauce and sprinkle with remaining cheddar cheese.

Bake for 20-25 minutes. Remove and serve immediately.

Tips for Perfect Stuffed Shells

Be sure not to over-cook your pasta shells. I usually pull my shells 1-2 minutes before the recommended cook time to make sure they don’t over-cook in the oven.
Don’t over-stuff your baked shells. You want your pasta shell full but not overflowing.
Spoon your cheese sauce over your stuffed shells. You don’t need them completely covered.
These shells make great leftovers! Store them in the refrigerator, covered, for up to 4 days.
I recommend boiling the entire package of pasta shells, even though we may not use them all. Some of them may tend to break during boiling and we want shells that are intact.
To make life easy, consider grabbing a package of pre-cooked baked pieces from the salad dressing aisle of you grocery store. They are life saving!

SUBSTITUTIONS

Pasta – Feel free to sub out the large pasta shells for manicotti or even roll the filling up in cooked lasagna noodles to make little popper pinwheels.
Jalapeno peppers – Want to dial down the spicy kick from the peppers? When shopping for your jalapenos, grab peppers that aren’t as ripe. They will be shiny and without stress fractures. The older the pepper, the spicier the kick.
Bacon – I love using pre-cooked bacon pieces from the salad aisle at my grocery store. Huge time and trouble saver. If you prefer to use ‘fresh’ bacon, simply line a large baking tray with foil and cook your bacon in a 400 degree oven for approximately 20 minutes or until cooked crispy.

Can You Make Stuffed Shells Ahead?

Yes—this is a great make-ahead dish and actually works really well for busy nights.

Assemble ahead of time – Fill the shells, place them in the baking dish, and cover with sauce. Cover tightly and refrigerate for up to 24 hours before baking.
Hold the topping until baking – If you’re adding extra cheese on top, you can wait to add it until just before it goes into the oven for the best melt and texture.
Bake from chilled – Let the dish sit at room temperature for about 20–30 minutes, then bake as directed. You may need to add an extra 5–10 minutes since it’s cold going in.
Freezer option – Assemble the shells (before baking), wrap tightly, and freeze for up to 2–3 months. Thaw overnight in the fridge before baking.
Keep it creamy – If the sauce thickens after chilling, stir in a small splash of milk or broth before baking to keep everything smooth and creamy.

Storing and Reheating Your Leftovers

Refrigerate properly – Let the stuffed shells cool completely, then store in an airtight container or tightly covered baking dish. Keep in the fridge for up to 3–4 days.
Freeze for longer storage – Place cooled leftovers in a freezer-safe container or wrap tightly in portions. Freeze for up to 2–3 months for best quality. Thaw overnight in the fridge before reheating.
Reheat in the oven (best method) – Cover with foil and bake at 325°F until heated through. Add a splash of milk or extra sauce if needed to keep it creamy and prevent drying out.
Reheat in the microwave (quick option) – Heat individual portions in short intervals, stirring or rotating between bursts to ensure even warming.
Keep it moist – Stuffed shells can dry out as they sit, so a little extra sauce or liquid before reheating helps bring them back to that creamy, baked-fresh texture.

MORE JALAPENO PEPPER RECIPES

Enjoy ♥ Heather