Gluten Free Cheese Sauce | For Queso, too!

This gluten free cheese sauce made from scratch is perfect for dipping, making into queso, and even making the easiest gluten free mac and cheese ever!

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Why this recipe works

I used to make a casserole-style baked macaroni and cheese every week, in a large batch, for my family. But this recipe makes a small batch of cheese sauce, whether you make it with a roux (that mixture of cooked butter and flour that thickens liquids) or without. No cheese sauce reheats perfectly, though, so it's nice to make it in small quantities.

And then, you can always serve The Picky Eater the plain pasta tossed with butter. Even though he does love cheese, and will gladly toss some plain shredded cheddar on top of his plain pasta. You could even try using the base of the cheese sauce, without the shredded cheese at the end, as a bechamel sauce substitute for ricotta cheese in our gluten free lasagna.

The only difference between cheese sauce you plan to use for a simple gluten free macaroni and cheese and cheese sauce for dipping is thickness. The recipe below includes instructions for how to add a bit more cheese to thicken your sauce if you're planning to use it over pasta—or as a topping for my gluten free chili recipe! Check out my vegan Alfredo sauce and gluten free Alfredo sauce if you need another option to serve to your party.

Troubleshooting cheese sauce

If you've ever shied away from making gluten free cheese sauce from scratch, maybe it was because you were afraid of making a roux. Or maybe it's because you tried once, and it was grainy. I can help!

Sometimes, you'll find a recipe for cheese sauce on a website, and there are commenters swearing that the recipe is awful because their sauce wasn't smooth. Instead, it was grainy. That's a terrible experience, but it's also generally user error.

When you heat milk, you must heat it very slowly over a very low flame, whisking often. If your milk is a bit on the older side, it's likely more acidic, which will make it much more likely to curdle when heated (even though it smells fine and isn't spoiled).

If you've added an acidic ingredient to your sauce, or cook it at a temperature that's a bit too high, it may curdle a bit. That just means that the milk proteins are clumping together.

It's unpleasant, but you can usually just skim the curdled clumps off the top. If you're making a pudding or custard, you can also blend the milk to smooth out the curds.

Can I reheat my cheese sauce?

Ideally, cheese sauce is eaten fresh, immediately after it's cooked. That is true for both roux-based sauce and no-roux sauce. But that doesn't mean you absolutely can't reheat it.

If you reheat your cheese sauce too quickly, it's likely to break and curdle. But if you reheat it very, very slowly on the lowest possible flame in a small saucepan on the stovetop, it should be fine.

Part of the reason that your sauce thickens as it stands is that some of the moisture will evaporate. Just add a splash more milk, and reheat slowly.

Better than reheating the sauce, though, is making this small batch. Then make the easy sauce again when you're ready for some more!

Gluten Free cheese sauce ingredients and substitutions

Dairy

I have tried so many dairy-free cheeses, and many are really good (Violife is great; Daiya has really stepped up their game), but none of them melt into a cheese sauce like the real thing. I just cannot recommend that you use any of them in this recipe.

If you're dairy-free, you really need a separate recipe for mac and cheese or cheese sauce for dipping as queso or plain. Years ago, one of my children was dairy-free for over a year and she really loved mac and cheese, so I tried and tried to develop a great recipe.

But I failed on my own. The very best dairy free mac and cheese sauce recipe I have ever tried is from my friend Alisa Fleming of Go Dairy Free from her book. She does have a recipe on her site for a dairy free cheese sauce, and it looks very similar to the one in her book. Use that!

Flours

I always have at least 2 cups of our gum-free gluten free flour blend in a sealed glass container in my pantry. It's useful for so very many things. But if you don't already have a batch of it made, I wouldn't bother making it so you have the single tablespoon of it for this recipe.

In its place, you can use an equal amount of superfine sweet white rice flour, or even cornstarch or arrowroot. The same goes for the cornstarch in the no-roux recipe.

Gluten Free Cheese Sauce Recipe

5 from 7 votes

By Nicole Hunn

Prep Time: 10 minutes mins

Cook Time: 10 minutes mins

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This gluten free cheese sauce made from scratch is perfect for dipping, making into queso, and even making the easiest mac and cheese ever!

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Ingredients 

1x2x3x

For roux-based cheese sauce

• ▢ 1 tablespoon (14 g) unsalted butter
• ▢ 1 tablespoon (9 g) gum free gluten free flour blend, (See Recipe Notes)
• ▢ ⅝ cup (5 fluid ounces) milk, plus more as necessary
• ▢ 4 ounces cheddar cheese, shredded (fresh, not preshredded) plus more as needed
• ▢ Salt and freshly ground pepper, to taste

For cheese sauce without a roux

• ▢ ½ cup (4 fluid ounces) milk, plus more as necessary
• ▢ 2 ounces cheddar cheese, shredded (fresh, not preshredded) plus more as needed
• ▢ 1 teaspoon cornstarch, (See Recipe Notes)
• ▢ 2 ounces Kraft deli deluxe American cheese slices, (about 3 slices) (See Recipe Notes)
• ▢ Salt and freshly ground pepper, to taste

For making macaroni and cheese

• ▢ 2 ounces dried gluten free elbow macaroni, cooked according to package directions and tossed with 1 tablespoon (14 g) unsalted butter, then set aside

For making queso

• ▢ Mexican salsa fresca/pico de gallo

Instructions 

For the roux-based cheese sauce.

• Melt 1 tablespoon butter in a small saucepan over medium-low heat. Add the flour (blend), and whisk until smooth.
• Cook slowly, whisking frequently, until the mixture is just beginning to brown, about 2 minutes or less. Pay close attention, as it will begin to change color very quickly.
• Add the milk, and whisk to combine. Continue to whisk to smooth out the clumped mixture, and cook until it just begins to simmer.
• Remove from the heat and add 4 ounces of the shredded cheese. (If you’re making macaroni and cheese, add the remaining 1 ounce of the cheese.)
• Mix until the cheese is melted and the mixture is smooth.
• If necessary to melt all of the cheese, return the saucepan to the stovetop over very low heat, mixing constantly. Add salt and/or pepper to taste.
• If you’re making macaroni and cheese, add the sauce to the cooked macaroni and butter, toss to coat and serve immediately.
• If you’re making plain cheese sauce, serve immediately.
• If you’re making queso, add the salsa, mix, and serve immediately.

For the no-roux cheese sauce.

• Place the milk in a small saucepan over very low heat. Bring to a simmer, whisking very frequently.
• Continue to cook until the milk just begins to reduce (about 3 minutes). If the milk curdles at all, try to skim any solids off the top.
• Toss 2 ounces of the shredded cheddar in the cornstarch, remove the saucepan from the heat, and add the cheese and starch to the hot milk. (If you’re making macaroni and cheese, add the remaining 1 ounce of the cheese.) Mix to combine.
• Tear the cheese slices into about 4 pieces each, and add them to the mixture, too. Mix until smooth.
• If necessary to melt all of the cheese, return the saucepan to the stovetop over very low heat, mixing constantly. Add salt and/or pepper to taste.
• If you’re making macaroni and cheese, add the sauce to the cooked macaroni and butter, toss to coat and serve immediately.
• If you’re making plain cheese sauce, serve immediately.
• If you’re making queso, add the salsa, mix, and serve immediately.

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Notes

For the GF flour and/or cornstarch

In place of the gum-free gluten free flour blend in the roux-based recipe, or the cornstarch in the no-roux recipe, you can use an equal amount of superfine sweet white rice flour, or even cornstarch or arrowroot.

For the Kraft deli deluxe American cheese slices

You know those extra- shiny slices of American cheese that are usually individually wrapped? We are not using those!

We are using the Kraft package that usually comes in a square blue package, and says “deli slices.” The deli slices have that rich American cheese taste and texture that helps add that creamy richness and thickness to the cheese sauce. But they are actually real cheese, not a “cheese product.”

They also come in American and cheddar flavors. I prefer the American flavor in this recipe, but it’s a matter of taste.

Nutrition information is automatically calculated, so should only be used as an approximation.

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