Butternut Squash Mac and Cheese

My Butternut Squash Mac and Cheese is comfort food with a gentle autumn twist. Roasted squash blends into the cheese sauce, making it silky and giving it a lovely golden colour, while sneaking a bit of veg into a family favourite.

It is built on a proper roux rather than blended squash, which is the less common way round and the reason the sauce stays a cheese sauce with a squash note rather than turning into a sweet vegetable puree. Other squash work just as well if that is what you have.

If you like a comforting bake, you will also enjoy my Hunters Chicken.

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Which Squash to Use

Here is a list of squash varieties that work very well in this dish:

• Butternut Squash: This is a popular choice due to its sweet, nutty flavour and smooth texture when cooked. It blends well into a puree and pairs nicely with the creamy cheese sauce.
• Acorn Squash: Slightly less sweet than butternut, acorn squash has a tender, yet slightly fibrous texture. It adds a beautiful colour and a more subtle squash flavour.
• Kabocha Squash: Also known as Japanese pumpkin, kabocha is sweeter than butternut. It has a rich, earthy flavour and a fluffy texture, which makes it a lovely addition to the dish.
• Delicata Squash: This variety is smaller and easier to handle. It has a creamy texture and a corn-like sweet flavour. Delicata squash’s thinner skin is also edible, though for this recipe, you’d typically remove the skin after roasting.

Pumpkin works too. It has much the same texture and sweetness once roasted and goes into the sauce the same way. Use a culinary variety rather than a carving pumpkin, which is watery and has very little flavour.

Choosing Cheese for Squash Mac and Cheese

For the Roasted Squash Mac and Cheese recipe, selecting the right cheese can significantly enhance the flavour and texture of the dish. Here are some excellent cheese options that pair well with the sweet, earthy notes of the squash:

• Mature Cheddar - A classic choice for mac and cheese, sharp cheddar adds a depth of flavour with its distinct tangy and slightly earthy taste. It melts well, making it ideal for a creamy sauce.
• Gruyère - This cheese offers a nutty, slightly sweet flavour. It melts beautifully, creating a smooth and velvety sauce, and complements the squash nicely.
• Parmesan - Grate some Parmesan into the mix for a more intense flavour. Its salty and slightly fruity taste adds a nice contrast to the sweetness of the squash.
• What to avoid - very young, very high-fat cheeses, and anything you have grated coarsely. Both are prone to stringing and to squeezing their fat out into the sauce. A well-aged cheese grated finely blends far better.

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Making the Sauce, and How to Stop It Going Grainy

The sauce is a plain bechamel: equal weights of butter and flour cooked together for a minute or two, then the milk whisked in gradually until it thickens. The cheese goes in after that, and everything that can go wrong with this dish goes wrong at that moment.

Heated past its melting point, cheese tightens into hard little clumps and pushes its fat out, which is the grainy, oily sauce people describe. Four things prevent it, and this recipe is already doing three of them. Grate the cheese finely so it disperses instead of sitting in lumps. Take the pan off the heat before the cheese goes in, and stir as little as you can get away with afterwards, because stirring pushes the protein back together. The flour in the roux is the third: starch coats those protein patches and keeps them apart, which is the real reason a roux-based sauce is more forgiving than a blended one.

The fourth is the teaspoon of lemon juice in the ingredient list, which looks like an odd addition and is doing more work than anything else in the pan. Cheese protein is held together by calcium; the acid strips that calcium away and leaves the proteins separate. It is the same reason a fondue is made with wine rather than water. If your sauce does tighten on you, another squeeze of lemon or a splash of white wine will often bring it back.

The mustard and the nutmeg are not optional garnishes either. Both are in the card because a cheese sauce with sweet squash in it goes flat without something sharp and something warm to push against.

Equipment You’ll Need

Ingredient Substitutions

• No butternut any of the squash above, or pumpkin. Frozen butternut chunks roast fine from frozen, they just need a few minutes longer and will not colour as hard.
• Gluten free swap the plain flour for cornflour, using about half the weight, and whisk it into cold milk before it goes near the heat rather than making a roux with it.
• No single cream whole milk works, and the sauce will be very slightly thinner. Do not use skimmed, which gives a watery sauce whatever you do to it.
• Dairy-free milk oat milk is the closest for a savoury sauce. Almond is thin and reads sweet against the squash.
• No panko ordinary breadcrumbs, or crushed crackers. Panko stays crisper for longer because the flakes are bigger and drier.
• No pumpkin seeds chopped walnuts or flaked almonds, toasted in the same butter. Or leave them out and use more panko.

How to Make Butternut Squash Mac and Cheese, Step by Step

Eight steps, matching the recipe card below exactly. The card is the version to cook from; this is the one that says why each step is the way it is.

1. Get the oven properly hot, 240C. That is hotter than most versions of this dish and it is deliberate: twenty minutes at a high heat colours the cut faces before the flesh has time to dry out, where a lower, longer roast gives you softer squash with less caramelisation. If your oven runs hot, or your pieces are small, look at them at fifteen minutes.
2. Roast the squash skin side down. Rub the pieces with oil and lay them cut side up on a parchment-lined tray, spread out rather than touching. The skin protects the flesh from the tray while the cut faces take the heat. Twenty minutes, until a knife goes through the thickest part without resistance and the edges have gone properly brown at the tips.
3. Make the roux and build the bechamel. Melt the butter in a small pan, stir in the flour and cook it over a low heat for a minute or two. You are cooking the raw taste out of the flour, not colouring it, so keep it pale. Then the milk, a little at a time, whisking each addition in fully before the next goes in. Add it all at once and you get lumps that no amount of whisking will fix afterwards.
4. Take it off the heat, then the cheese. Half the cheddar, finely grated, stirred through until it melts, and then the cream, lemon juice, nutmeg, pepper and salt. The pan comes off the heat first on purpose: cheese held above its melting point clumps and pushes its fat out, which is the grainy sauce everyone complains about. Stir it as little as you can get away with. Set it aside.
5. Blend the squash and drop the oven to 200C. Scoop the flesh away from the skin while it is still warm, which is far easier than doing it cold, and blend it smooth. A tablespoon of water helps it come together if it is stiff. The oven comes down because the dish is now baking rather than roasting, and 240C would burn the cheese on top long before the middle is hot.
6. Fold, assemble and bake. Half to two thirds of a cup of the puree into the sauce, which is enough to colour it and sweeten it without turning it into squash soup. Fold through the cooked macaroni, into the dish, the rest of the cheese over the top, and 25 to 30 minutes. Keep the sauce looser than looks right when you assemble it, because the pasta goes on drinking liquid in the oven.
7. Toast the topping while it bakes. Butter in a pan, then the panko and pumpkin seeds, stirring the whole time until they are golden. This takes about three minutes and it goes from golden to burnt in the last thirty seconds, so do not walk away. Toasting it separately rather than scattering it raw over the dish is why it stays crunchy.
8. Top it at the table, not before. Scatter the crumbs and seeds over the baked dish just as it goes out, with parsley or thyme if you have it. Put them on before baking and they soften in the steam coming off the sauce, which is exactly what you were trying to avoid.

Recipe Card for Butternut Squash Mac and Cheese

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What to Do With the Rest of the Squash

The recipe roasts half a butternut and uses half to two thirds of a cup of the puree, so you will have some left over. That is on purpose rather than an oversight: more squash than that and the sauce starts tasting sweet rather than cheesy, which is the single most common complaint about this style of recipe.

What is left keeps for four days in the fridge and freezes for three months. It thins into a soup with hot stock and a little cream, goes through a risotto near the end, sits under a fried egg on toast, or gets stirred into a pasta sauce the same way it went into this one.

Storing, Freezing and Reheating

Cool it quickly rather than leaving the dish out, and it keeps for three days in the fridge. It freezes for three months, either as a whole dish or in portions, and it comes back better than most baked pasta because the sauce is starch-stabilised rather than a plain cheese melt.

Reheat covered, with a splash of milk stirred in first, because the pasta will have drunk a good deal of the sauce overnight. It wants to be piping hot through rather than warm. Add the crunchy topping fresh each time: it will not survive the fridge, and it takes three minutes to make.

To make it ahead, assemble the dish the day before and keep it covered in the fridge, then bake it from cold with an extra five to ten minutes. Toast the topping on the day.

FAQ for Butternut Squash Mac and Cheese

Can I make it ahead of time?

Yes. Assemble it, cover, and keep it in the fridge for up to a day, then bake (add a few extra minutes as it starts cold). It also reheats well - add a splash of milk to loosen the sauce.

Can I freeze it?

Yes, it freezes well for up to 3 months. Thaw in the fridge overnight and reheat until piping hot, adding a little milk if it looks dry.

What cheese works best?

A good melting cheese like mature cheddar is the base; a handful of Parmesan or Gruyère adds extra savoury depth.

How do I stop it drying out?

Keep the sauce a little looser than you think - it thickens as it bakes - and do not overbake. A splash of milk when reheating brings it back to creamy.

Can I sneak in more veg?

Absolutely. Stir a handful of spinach through the sauce, or use wholemeal pasta, for an easy lift.

Do I have to roast the squash, or is there a shortcut?

Roasting gives the deepest, sweet, caramelised flavour, but if you are short on time you can steam or microwave the squash until soft and mash it - plenty of readers do this and still get a lovely creamy sauce.

My sauce is too thin. What do I do?

Let it bubble gently for a few more minutes before the pasta goes in, stirring, and it will tighten. Do not add more flour to a finished sauce, because it has no chance to cook out and you will taste it. Remember that it thickens again in the oven and again as it stands, so a sauce that looks slightly loose at the assembly stage is right.

My sauce is too thick. What do I do?

Whisk in more milk, a splash at a time, off the heat. This is far more common than it sounds because flour keeps thickening as it cools, so a sauce that seemed right in the pan can be a paste by the time the pasta is drained.

The sauce went grainy or oily. Can I save it?

Often, yes. Take it off the heat, add a squeeze of lemon juice or a splash of white wine, and stir gently. The acid pulls apart the calcium bonds holding the cheese protein together. Next time, take the pan off the heat before the cheese goes in, grate the cheese finely, and stir it as little as possible once it is in.

Is 240C not too hot for roasting squash?

It is hotter than most recipes, which sit around 200 to 220C, and that is a choice rather than a mistake. Twenty minutes at a high heat browns the cut faces properly while the flesh stays moist. Lower and longer gives you softer squash and less caramelisation, which is also a perfectly good result if you prefer it. If your oven runs hot, check at fifteen minutes.

A Few Words from the Chef

This is one we make at work when the squashes come in, and it is at its best when the squash is my own. It is a seasonal thing for me rather than something I make all year. Tell me how you got on with it, and whether you went heavier on the squash than I do.