Clean Eating Jalapeño Popper Mac and Cheese

4.50 from 4 votes

When the two meet, it's love at first bite.

On the hunt for healthy jalapeño poppers? How about clean eating mac and cheese? If you’ve nearly given up on your hopes of enjoying these two dishes in a healthy way, we’ve come to your rescue! You’ll love this jalapeño popper mac and cheese, made with clean ingredients to keep the calories down and the flavor delicious. A creamy low-fat cheese sauce and crunchy whole wheat bread crumbs give it the crunch and flavor you love, but add healthful protein and fiber normally not found in a dish like this. The end result is a meal that will satisfy you, while helping you stick to your diet.

More Mac & Cheese Recipes:
Mac & Cheese with Sun-Dried Tomatoes
Tex-Mex Style Macaroni and Cheese
Slow Cooker Macaroni and Cheese

4.50 from 4 votes

Clean Eating Jalapeño Popper Mac and Cheese

Stay on your healthy-eating plan and keep enjoying your favorite foods with this amazingly delicious Mac and Cheese dish.
Prep Time 15 minutes
Cook Time 30 minutes
Total Time 45 minutes
Yield 6 people
Serving Size 0.75 cup
Course Dinner
Cuisine American
Author SkinnyMs.


  • 3 cups whole-grain macaroni noodles dry, cooked according to the package directions
  • 2 tablespoons olive oil
  • 1 onion small, diced
  • 2 jalapeño peppers seeded and diced
  • 1 garlic clove minced
  • 1 teaspoon mustard powder or 1 tablespoon prepared mustard
  • 2 tablespoons flour I used white whole-wheat
  • 2 cups milk low-fat
  • 2 cups colby jack cheese low-fat
  • 4 ounces cream cheese low-fat
  • 1/2 cup whole-wheat bread crumbs
  • salt and pepper to taste


  • Preheat oven to 400 degrees F.
  • In a large saucepan, heat the olive oil over medium heat. Add the onions and jalapeños and cook until soft, about 5 minutes. Add the garlic and continue cooking 1 more minute. Stir in the mustard powder and flour and season with salt and pepper. Stir for 1 minute.
  • Add the milk and bring to a boil, whisking constantly. Boil for 1 minute and turn off heat. Stir in 1 1/2 cups of the Colby jack and all of the cream cheese. Add the cooked pasta and stir until well coated. Transfer to a casserole dish.
  • Top with breadcrumbs and remaining cheese and bake for 30-35 minutes until top is browned and cheese is bubbly. Allow to stand for 5 minutes before serving.

Nutrition Information

Serving: 0.75cup | Calories: 351kcal | Carbohydrates: 34g | Protein: 22g | Fat: 14g | Saturated Fat: 5g | Cholesterol: 30mg | Sodium: 496mg | Fiber: 5g | Sugar: 6g |
SmartPoints (Freestyle): 11
Keywords Pasta, Vegetarian

Have you made this recipe?
Tag @skinnyms on Instagram or hashtag it #skinnyms

Be sure to subscribe to our newsletter, like our Facebook page, and follow us on Pinterest for tasty recipes, clean eating tips, and healthy lifestyle resources.

What are some of your favorite Skinny Ms. healthy comfort food recipes? How about clean eating dishes that bring the spice and the crunch? Fill us in on your favorite recipes below.

This post may include affiliate links.


The SkinnyMs. team believes that all people, regardless of age, size, and fitness level, have the power to transform their lives — they just need the resources to do so. The SkinnyMs. method promotes healthy living through a combination of clean eating and regular exercise. We offer everything you need to be successful.

More by Skinny


    1. That's cheese for you, haha! 🙂 Hey, there is no problem with an indulgence every now and again, right? 🙂

  1. Is low fat cheese really clean? When I am going to indulge, I always buy the full fat cheese because I assume they need chemicals to make it low fat.

    Any insight on this?

    1. Tracy, Low-fat or Whole-fat…that is the question. Both have pros and cons. All milk, with the exception of raw, go through a processing before arriving at the supermarket. Skim does have the fat removed, which some people believe is needed in a healthy diet. On the other hand, many experts believe low-fat has greater benefits because of less fat. We typically use low-fat dairy because of the obesity epidemic and its subsequent disease causing factors. It really has to be a personal choice. Feel free to substitute full-fat dairy for low-fat. It will work just as well in any of our recipes. 🙂

  2. I’m wondering if I can sub Colby jack for a blend of sharp cheddar and pepper jack? That’s what I have on hand in the cheese drawer!

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating