Ultimate Freezer-Friendly Butternut Squash Mac and Cheese: Instant Pot & Stovetop Recipe
This Freezer-Friendly Instant Pot Butternut Squash Mac and Cheese offers a delightful fall-inspired twist on a beloved comfort food classic. Combining the creamy goodness of macaroni and cheese with the subtly sweet and earthy flavor of butternut squash, this dish is not only incredibly delicious but also packed with nutrients. Whether you’re a busy weeknight warrior or planning ahead for delicious meals, this recipe’s freezer-friendly nature makes it an absolute game-changer. It’s an ideal way to enjoy a hearty, homemade meal with minimal effort when you need it most, providing a wholesome alternative to traditional mac and cheese without sacrificing any of the comforting richness.

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Ingredients and Substitutions for Butternut Squash Mac and Cheese
Crafting the perfect Butternut Squash Mac and Cheese involves a careful selection of ingredients, but don’t worry, there are plenty of easy substitutions to fit your pantry and dietary needs. Here’s a detailed look at what you’ll need and how to adapt it:
- Olive oil: This forms the base for sautéing, adding a subtle richness. Any neutral oil, such as avocado oil, vegetable oil, or grapeseed oil, can be used effectively.
- Yellow onion: Diced yellow onion provides a foundational aromatic flavor. Feel free to substitute with white or red onions for a slightly different pungency, or even use onion powder (about 1 teaspoon per medium onion) or dried onion flakes in a pinch.
- Garlic cloves: Freshly minced garlic delivers the best flavor. However, store-bought minced garlic works wonderfully for convenience. If you’re out of fresh garlic, you can use garlic powder (1/2 teaspoon per clove), granulated garlic, or garlic flakes.
- Salt & pepper: Essential for seasoning. Adjust these to your personal taste, adding more as needed to enhance the overall flavor profile of the dish.
- Water or chicken broth: The liquid base for cooking the pasta. Vegetable broth is an excellent alternative, maintaining a vegetarian profile. Other stocks like turkey or beef can also be used for a deeper flavor. Both store-bought and homemade broths or stocks are suitable. The broth infuses the pasta with flavor as it cooks.
- Macaroni pasta: The classic choice for mac and cheese, providing that iconic shape that holds the sauce perfectly. If traditional macaroni isn’t available, consider other small, shapely pasta types like penne, gemelli, fusilli, ditalini, or even shells. For a gluten-free option, use your preferred gluten-free pasta, ensuring it’s cooked according to package directions as cooking times may vary.
- Butternut squash: This star ingredient adds sweetness, creaminess, and a beautiful autumnal hue. You can use freshly diced butternut squash (about 1 cup once peeled and seeded) or defrosted frozen butternut squash cubes. Ensure frozen squash is fully thawed before cooking to maintain proper moisture balance.
- Milk: Crucial for the creamy sauce. Use your preferred type of milk, whether it’s whole milk for extra richness, 2% milk, or dairy-free alternatives like lactose-free milk, almond milk, oat milk, or cashew milk. The fat content of the milk will impact the final creaminess, so choose accordingly.
- Mozzarella or Swiss cheese: These cheeses are chosen for their excellent melting properties, contributing to a wonderfully gooey, stretchy texture. Both hand-grated and pre-packaged grated varieties work well. Other great melting cheeses you could try include Gouda, Provolone, or Gruyère, each offering a unique flavor twist.
- Sharp cheddar cheese: A key ingredient for that distinct mac and cheese tang and depth of flavor. Whether you grate it yourself or use pre-shredded, cheddar is essential. For a smoky note, consider smoked cheddar. Other hard or semi-hard cheeses like Parmesan, Monterey Jack, or even a mild Colby can be used for variation.
- Thyme: Fresh thyme adds an aromatic, slightly earthy flavor that complements the squash beautifully. Fresh oregano, basil, or marjoram are excellent herbal substitutions that provide similar aromatic qualities.
- Sage: Another classic fall herb that pairs wonderfully with butternut squash. Rosemary offers a robust, piney alternative, while tarragon provides a subtle anise flavor. Bay leaves or a good quality poultry seasoning blend can also work if you’re looking for an aromatic substitute.
- Chives: Used for a fresh, mild oniony garnish and a pop of color. Scallions (green onions), finely diced shallots, leeks, or even a very small amount of finely minced yellow onion can be used to achieve a similar fresh finish.

Stovetop Butternut Squash Mac and Cheese Method
While the Instant Pot offers unparalleled speed and convenience, you can certainly achieve a fantastic Butternut Squash Mac and Cheese on the stovetop. This method also works as a “one-pot” approach, making cleanup straightforward. The key is to manage your liquid and cooking times carefully. You’ll begin by sautéing your aromatics (onion and garlic) directly in the saucepan. Then, you’ll add the pasta along with the broth or water, allowing the pasta to cook and absorb the liquid, infusing it with flavor. Once the pasta is tender and the liquid is mostly absorbed, you’ll stir in your prepared butternut squash sauce (or homemade puree if you’re starting from whole squash) and the various cheeses until everything is melted, creamy, and wonderfully combined. This method provides a hands-on cooking experience, allowing you to monitor the sauce’s consistency and pasta’s doneness precisely.
Storing and Reheating Your Butternut Squash Mac and Cheese
Proper storage is key to enjoying your delicious mac and cheese for days to come. Once your Butternut Squash Mac and Cheese is cooked and has cooled completely to room temperature, transfer it to an airtight container. It can be safely refrigerated for up to 3-5 days. When you’re ready for another comforting serving, reheating is simple. For microwave reheating, sprinkle about 1-2 tablespoons of water over your portion. This extra moisture is crucial to prevent the pasta from drying out and helps reactivate the creamy sauce. Heat it in the microwave for 2-3 minutes, stirring thoroughly every 40-50 seconds, until it’s heated through and creamy again. For an extra touch of indulgence, consider stirring in a small knob of butter and garnishing with some freshly grated cheese or chopped fresh herbs before serving.

Freezing Butternut Squash Mac and Cheese for Convenient Meals
One of the most impressive features of this Butternut Squash Mac and Cheese is its excellent freezer-friendliness. This makes it an ideal choice for meal prepping and ensures you always have a comforting, homemade meal on hand for busy days. You can freeze individual portions for up to 3 months, making it perfect for grab-and-go lunches or quick dinners. I highly recommend freezing in foil containers specifically designed for individual servings. These containers allow you to take a single portion directly from the freezer and pop it straight into a preheated 400°F (200°C) oven for about 30 minutes, or until bubbling hot and thoroughly reheated. This saves immensely on dishes and prep time. Alternatively, if reheating in the microwave, sprinkle about a tablespoon of water over the frozen mac and cheese before microwaving for approximately 3 minutes, stirring halfway through, to ensure it stays creamy and moist. I can personally attest to its deliciousness even after freezing; I once enjoyed this mac and cheese for five days straight without any decline in quality, leaving no freezer leftovers!
Freezing the Butternut Squash Puree for Future Recipes
Beyond freezing the entire mac and cheese dish, you can also prepare and freeze extra butternut squash puree to streamline future cooking. This is a fantastic strategy for efficient meal prep. To do so, simply make your puree following the recipe steps, then allow it to cool completely to room temperature. Once cooled, transfer the puree into an airtight, freezer-safe bag or container. For even easier portioning, you can freeze it in ice cube trays and then transfer the frozen cubes to a larger bag. This method allows you to grab just the amount you need for a recipe. Properly stored, the puree can be kept in the freezer for up to 5-6 months. When you’re ready to use it, simply transfer the frozen puree to the refrigerator and let it defrost overnight. Having this versatile puree on hand makes whipping up this mac and cheese, or adding a nutritional boost to soups, sauces, or smoothies, incredibly fast and convenient.

More Freezer-Friendly Meal Ideas
If you love the convenience of freezer meals, here are some other fantastic recipes that can be prepped in advance:
- Freezer-friendly Meal Prep: Baked Turkey Meatballs – Perfect for quick protein additions to any meal.
- Freezer Meal: Chicken Pasta Bake – Another comforting pasta dish that freezes and reheats beautifully.
- Instant Pot Honey Garlic Chicken Meal Prep Bowls – Delicious and flavorful, ideal for weekly meal prep.
Essential Meal Prep Tools
Having the right tools can make your meal prepping experience even smoother, especially when preparing freezer-friendly dishes like this Butternut Squash Mac and Cheese:
- Investing in quality glass meal prep bowls is highly recommended. They are perfect for portioning out your pasta for freezing and then easily defrosting and reheating in the microwave. They’re also great for general food storage.
- For those who prefer oven reheating directly from the freezer, these aluminum foil containers are an absolute lifesaver. They are designed for convenience, allowing you to move your prepped meals from freezer to oven seamlessly, eliminating the need for extra dishes.

Freezer-Friendly Butternut Squash Mac & Cheese
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Ingredients
- 1 tbsp olive oil
- 1 yellow onion, diced
- 2 cloves garlic minced
- 1/2 tsp salt
- 1/4 tsp pepper
- 3 cups water or chicken broth
- 1 lb dry macaroni pasta
- 1 cup butternut squash, cut into cubes
- 1/2 cup milk
- 1 cup mozzarella or Swiss cheese, grated
- 2 cups sharp cheddar cheese, grated
- Fresh thyme/sage/chives for garnishing *optional*
Instructions
Instant Pot Method
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Add olive oil, diced onion, minced garlic, salt & pepper, water or chicken broth, and dry macaroni pasta to the Instant Pot in the specified order. Ensure the pasta is mostly submerged in the liquid. Secure the lid, set the valve to sealing, and cook on high pressure for 3 minutes. After cooking, perform a quick release of pressure according to your Instant Pot’s instructions.
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While the pasta cooks, preheat your oven to 425°F (220°C). Toss 1 cup of butternut squash cubes with a drizzle of olive oil, then spread them on a baking sheet and roast for 30 minutes, or until tender and slightly caramelized. Once roasted, transfer the squash to a blender, add 1/2 cup milk, and blend until smooth to create a creamy puree.
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Once the Instant Pot is safe to open, remove the lid. Stir the prepared butternut squash puree into the cooked pasta, along with the grated mozzarella (or Swiss cheese) and sharp cheddar cheese. Continue stirring until all the cheeses are melted and the sauce is smooth and creamy. Serve immediately in bowls, garnished with fresh chives, sage, or thyme as desired. Enjoy your homemade, comforting Instant Pot Butternut Squash Mac and Cheese!
Stovetop Method
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In a large saucepan or Dutch oven, heat 1 tablespoon of olive oil over medium-high heat. Add the diced yellow onion and sauté for about 5 minutes, or until it softens and becomes translucent. Stir in the minced garlic, salt, and pepper, cooking for another minute until fragrant. Pour in 3 cups of water or chicken broth and add the dry macaroni pasta, stirring well to ensure the pasta is evenly distributed and mostly submerged. Bring the mixture to a boil, then reduce heat to medium-low, cover, and let it simmer for 12-15 minutes, or until the pasta is al dente and most of the liquid has been absorbed. Stir occasionally to prevent sticking.
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Meanwhile, preheat your oven to 425°F (220°C). Arrange 1 cup of butternut squash cubes on a baking sheet, drizzle with olive oil, and roast for 30 minutes until soft and slightly caramelized. Once roasted, transfer the cooked squash to a blender along with 1/2 cup of milk. Blend until a smooth, creamy puree is formed.
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Once the pasta is cooked and the liquid absorbed, remove the saucepan from the heat. Stir in the prepared butternut squash puree, grated mozzarella (or Swiss cheese), and sharp cheddar cheese. Mix thoroughly until all the cheese has melted into a rich, creamy sauce. Serve this delicious stovetop butternut squash mac and cheese immediately, garnished with fresh chives, sage, or thyme for added flavor and visual appeal. Enjoy this comforting and wholesome meal!
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