This Gluten Free Hidden Vegan Healthy Macaroni and Cheese is by far my favorite mac and cheese. It’s made with a cream cheese sauce and has veggies in it! It’s suitable for kids and adults alike and it’s delicious!
Absolutely no one can say you sneaked cauliflower and butternut squash into this delicious macaroni and cheese sauce!
Gluten-Free Macaroni and Cheese with Pecan Crumbs
this Hidden Veggie Gluten Free Macaroni and Cheese is the perfect alternative to traditional macaroni and cheese. Sneak these veggies into a cream cheese sauce (even better if you add broccoli) and you’ve got the perfect sneaky healthy comfort food.
This recipe is ready in just 30 minutes and makes for a hearty, creamy and comforting pasta dinner! No one will know it’s made with vegetables! We all love this dish!
Ingredients needed for Macaroni and Cheese:
This easy macaroni and cheese recipe is full of delicious ingredients and of course hidden veggies! Here is what you need:
Cream Cheese Sauce
- Butternut Squash and Cauliflower: Cooked and mixed squash and cauliflower create a super creamy base for the cheese sauce. Plus, hidden vegetables!
- olive oil: Use to brown squash and cauliflower for a little extra flavor before steaming.
- seasoning: An easy way to add flavor to a cheese sauce. Don’t skip the cinnamon. Trust me!
- Vegetable Soup and Milk: Add flavor and richness, and dilute cheese sauces into sauces!
- cheese: I used shredded parmesan and shredded cheddar to make the cheese sauce more cheesy.
- butter: Adds flavor depth to the sauce.
- Dijon Mustard: Provides a bit of tangy spice to the tangy sauce.
other ingredients
- spaghetti: I use 1 lb gluten free pasta. Use only your favorites! Not gluten free? Regular pasta is great too!
- broccoli: Broccoli doesn’t hide like other vegetables, but the cheese on top is enough to fool the kids! You can completely ignore this!
- Extra cheese: We add more cheddar and parmesan to the macaroni and cheese because you can never go wrong with more cheese, right? !
Pecan Crumbs
A fun traditional breadcrumb that’s easy, delicious, and nutritious!
- Pecan slices: You can easily make pecan slices by grinding them in a food processor until they reach a sandy consistency.
- seasoning: Give the pecan breadcrumbs some extra flavor with a simple mixture of paprika, paprika, garlic powder, and sea salt.
How to Make Healthy Macaroni and Cheese
This easy and kid-friendly dinner is ready in just 30 minutes!
- To cook vegetables: In a large frying pan, heat the oil, then add the squash, cauliflower, salt, pepper, and cinnamon. Cook until fragrant, then add vegetable stock and cover. Simmer for 8-10 minutes.
- To cook the pasta and broccoli: Cook gluten-free pasta according to package directions, then steam broccoli florets. Put the pasta under cold water and drizzle with a little oil.
- Make the sauce: In a high-speed blender, combine squash, cauliflower, and vegetable stock. Add cheese, milk, butter and mustard, then whisk until creamy.
- bake: In a large bowl, combine cooked pasta, steamed broccoli, and cheese sauce. Transfer macaroni and cheese to a baking sheet, top with cheddar and parmesan and bake at 350ºF for 10 minutes.
- Top, Roast and Serve: In a food processor, combine pecans, cayenne pepper, paprika, garlic powder, and sea salt. Sprinkle pecan crumbs over macaroni and cheese and bake until golden brown.
What’s the best cheese for mac and cheese?
I like to use a combination of shredded cheddar and parmesan to give this vegetable and cheesy cheese the flavor and texture.
However, any creamy and melted cheese is great! Try Gouda, Gruyere, Brie, Goat and more.

Do gluten free macaroni taste the same as cheese?
Yes! Of course, this cheese sauce has hidden veggies, so it won’t taste like the macaroni and cheese you get out of the box. But for homemade, I think it’s better! You still get that rich, creamy, delicious cheese sauce, but with all the health benefits of veggies combined.
As far as gluten-free noodles go, the texture will never be exactly the same as regular flour pasta, but you can definitely find very similar varieties.
This macaroni and cheese might be healthier, but we’re not sacrificing any flavor here!
Pecan Crumbs!
A handful of pecans (about 19 halves) are a good source of fiber, thiamine, zinc, and an excellent source of copper and manganese—a mineral essential for metabolism and bone health.
Pecans are also high in protein, and in each 1-ounce serving, you’ll get 12 grams of “good” monounsaturated fat, and zero cholesterol or sodium, making this dish even more nutritious!

Tips and Precautions
- Shred your own cheese. Pre-shredded cheese contains an anti-caking agent that creates a tough texture when melted. For the ultimate creaminess, chop your own.
- Make it more tacky. Feel free to add as much (or as little) cheese as you want to the cheese sauce. Make it your own!
- steamed broccoli, Cut it into florets and insert the steamer into the pot. Add water, cover, bring to a boil, and place the florets in the pot. Steam for 4-5 minutes or until fork tender. Drain and run under cold water to stop the cooking process.
- Cooked pasta is al dente. Since we are also baking pasta, I recommend cooking it according to package directions to avoid overcooking it in the oven.
- Add more vegetables. If you don’t really want to hide the veggies, feel free to add more to the broccoli macaroni and cheese. Peas, mushrooms, bell peppers, you name it!
- Leftover crumbs? they will be delicious too Grilled Salmon, roasted vegetables, Braised Artichokes, stuffed peppersin a salad, or as a breadcrumb mix Eggplant Parmesan.
Service suggestion
You can serve this vegetable macaroni and cheese on its own as a meatless main dish, or use it as a side dish next to your favorite protein.
How to store
Leftover gluten-free macaroni and cheese will keep for 3-5 days in an airtight container in the refrigerator. To reheat, warm in the microwave or on the stove with a little broth to moisten.
More Cheesy Pasta Recipes
Watch the video:
Gluten-Free Hidden Minestrone and Cheese with Pecan Crumbs
This Gluten Free Hidden Vegan Healthy Macaroni and Cheese is by far my favorite mac and cheese. It’s made with a cream cheese sauce and has veggies in it! It’s suitable for kids and adults alike and it’s delicious!
- Preparation time: 10 minutes
- Cooking time: 30 minutes
- total time: 40 minutes
- yield: 8 1X
Cream Cheese Sauce:
- 2 heaping cups butternut squash, diced
- 2 heaping cups cauliflower florets, chopped small
- 1 tablespoon Extra virgin olive oil
- 1/2 teaspoon Sea salt, more to taste
- 1/2 teaspoon black pepper, more to taste
- 1/4 teaspoon cinnamon, more to taste
- 1 cup vegetable soup
- 1 cup non-dairy milk of choice, use more if your sauce looks thick
- 1/2 cup Cheddar cheese, more as needed, more for topping
- 1/2 cup Parmesan cheese, more as needed, more for topping
- 3 tablespoons grass fed butter
- 1 teaspoon Dijon mustard
Other ingredients:
- 1 16-ounce package gluten-free pasta, cooked according to package directions
- 2 cups Broccoli florets, steamed (see note)
- 1/3 cup extra cheese, for topping
- Pecan Crumbs:
- 1/2 cup Pecan slices, finely ground in a food processor to a sandy consistency
- 1/4 teaspoon chili
- 1/4 teaspoon paprika
- 1/2 teaspoon garlic powder
- pinch of fine sea salt
- Heat extra virgin olive oil in a large saucepan over medium-high heat. Add butternut squash, cauliflower, sea salt, black pepper, and cinnamon. Cook for 1-2 minutes or until fragrant. Pour in the vegetable stock and cover the pot. Cook for 8-10 minutes, or until the vegetables are tender. Remove from heat and cool.
- When the butternut squash is cooked, cook the pasta according to package directions, then steam the broccoli. After the pasta is cooked, strain and run it under cold water to stop the cooking process. Mix with a little extra virgin olive oil to keep the pasta from sticking and set aside.
- Add the butternut squash, cauliflower, and remaining vegetable stock to a high-speed blender. Add cheese, non-dairy milk, 3 tablespoons grass-fed butter, and Dijon mustard. Stir until creamy. Taste and adjust seasonings as needed.
- Combine pasta and steamed broccoli in a large mixing bowl. Pour sauce over pasta and broccoli 1/2 cup at a time until pasta is thickly coated with sauce and cheesy to your liking. Taste and adjust salt and pepper as needed!
- Preheat oven to 350°F. Pour the macaroni and cheese into the baking pan. Top with extra cheddar and parmesan and bake for 10 minutes, until cheese is melted.
- While Mac & Cheese bakes, make pecan crumbs: Whisk the pecans in a food processor until they reach a sandy consistency. If using, mix in optional spices.
- When the macaroni and cheese are done, sprinkle with pecan crumbs and bake on low for 2-3 minutes, or until golden brown.
- Serve and enjoy!
notes
- Feel free to add more cheese as you taste the sauce!
- You can omit the paprika, paprika and garlic powder in the pecan topping if desired!
- Cheese sauce makes 4 cups. You may have about 1 cup leftovers, depending on how cheesy you like your macaroni and cheese! Store leftover cheese sauce in the refrigerator for up to a week.
- Steamed Broccoli: Cut broccoli into 2-inch florets. Insert the steamer basket into the medium pot. Add a little water, put the lid on, and bring the water to a boil. Add the broccoli florets to the pot and steam for 4 to 5 minutes, or until fork tender. Drain and run under cold water to stop the cooking process. Add pasta when cooked.
Nutrition
- Serving Size: 8
- Calories: 467
- sugar: 4.2 grams
- sodium: 429 mg
- fat: 37.5 grams
- Saturated fat: 9 grams
- carbohydrate: 24.3 hours
- fiber: 7.1 grams
- protein: 14.1 grams
- cholesterol: 29 mg
This article was originally published in 2017 with American Pecan Council. All thoughts and opinions are always 100% my own! I love pecans and the farmers who grow them! Thank you for continuing to support the LCK and the brands I work with!



