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Gluten Free Baked Macaroni and Cheese with Toasted Sunflower Seed Crust

Noodle nirvana. Comfort food. There’s nothing like a dish of hot bubbling macaroni and cheese to make you feel warm and cozy. This one features gluten free penne pasta, plenty of sharp cheddar cheese and a delicious surprise topping of toasted sunflower seeds!

Dishing out the macaroni and cheese from a red casserole dish using a wooden spoon

Macaroni and cheese. Simply a casserole of grated sharp cheese melted into sauce, stirred into hot cooked noodles, and baked with something crunchy on top. It’s basic sustenance—and easy to make from scratch.

Click here to PIN Gluten Free Sunflower Crusted Macaroni and Cheese!

Switching out three ingredients makes this macaroni and cheese gluten-free:

  • The pasta: Trader Joe’s sell an excellent gluten free brown rice penne pasta that holds together when cooked, unlike some gluten free pastas that break apart when they get near boiling water. Unless you read the label you would never know this product is gluten free. (see note)
  • The roux: Brown rice flour (affiliate link) blends with butter and thickens a sauce the same way as all purpose flour.
  • The crust: Simply sunflower seeds, toasted and ground in the blender. Unbelievably scrumptious—gluten free or not–you want this as the topping on your mac and cheese.
closeup photo of gooey macaroni and Cheese in a wooden spoon

One more changeup: In this recipe, the liquid is vegetable broth instead of milk. I think you’ll agree that this vegetable broth based “white” sauce has more flavor. And when you stir in all the cheese… nirvana.

ingredients for Macaroni and Cheese: pasta, butter, vegetable broth, cheese, and brown rice flour

Random pasta notes:

  • If you tolerate gluten, you can make this mac and cheese using wheat noodles. Likewise, you can use wheat flour in place of brown rice flour. But don’t skip the toasted sunflower seed topping–you will love it!
  • Don’t live near a Trader Joe’s? These brown rice pasta shells (affiliate link) would be a good substitute—same ingredients—just brown rice and water.

More yummy gluten-free pasta recipes:

Just so you know, a couple of the links above are affiliates. When you purchase products via my links, it doesn’t cost you anything and I earn a tiny commission, which helps me continue to provide free content here on Letty’s Kitchen. Thank you!!

Growing up, macaroni and cheese showed up on the dinner table menu many a Friday night. Mom’s macaroni and cheese was homemade, not from a box.

This recipe is very much like the mac and cheese I ate as a kid. Same technique–except made gluten free. First you make a roux of rice flour and butter to thicken the sauce. Next whisk in liquid, usually milk, but here we use vegetable broth. Next melt in the cheese and stir cooked gluten free pasta. Scrape into a buttered casserole dish. Cover with a crunchy topping and bake until bubbling.

Typically, there’s a layer of buttery breadcrumbs on top–Mom put wheat germ and butter on hers. My topping of toasted sunflower seeds adds protein and keeps this baked mac and cheese gluten free.

Mom seasoned macaroni and cheese with a dash of Worcestershire sauce and a little bit of garlic powder. With the vegetable broth base you don’t need either. Since it’s the way I learned, I’d probably add the Worcestershire, except the ingredient list includes anchovies so it’s not vegetarian, and now they put freeking corn syrup in it!

Macaroni and Cheese from the oven ready to eat in red casserole dish

The other night, I tried a macaroni and cheese with butternut squash recipe. It reminded me of this mac and cheese recipe with the unique crunchy crust, so instead of a panko crust, I used my topping. So good! This post is an update of the original from 2014! Enjoy!

When the world has got me down and I need gooey cheesy comfort food—I head to the kitchen and whip up homemade mac and cheese. Especially this one. I feel better even before it starts to bubble in the oven.

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PS If you make this recipe and love it, please consider leaving a blog post comment. Your comments help other readers learn more about the recipe. If you’d also give the recipe a ✮✮✮✮✮ rating, I’d be even more delighted!


  • I’m headed to TJ’s today! And love the idea of a sunflower crust- nuts and seeds for the win! Reply · 21 October, 2014

    • Letty

      Thanks Kelley! We are lucky to have that TJ store (fairly) close by. And I thought they would never come–liquor laws. So they don’t sell 2 buck chuck–who cares. Reply · 21 October, 2014

  • Dennis Halloran

    Makes me want to wander in the 219 Kitchen Reply · 21 October, 2014

    • Letty

      It’s a great recipe–thanks Mom! and Denny! Reply · 21 October, 2014

  • I know it’s not polite to tell someone what they should do, but… you SHOULD totally enter that recipe into a contest. I’ve seen a lot of mac and crack recipes and have never seen anything sound so innovative and scrumptious. KUDOS!! Reply · 23 October, 2014

    • Letty

      Thanks Jenny!!! Now I gotta find that contest….
      It’s polite as all get out to send someone kudos and should suggestions– I appreciate it! Reply · 23 October, 2014

  • It’s good to update the classics and keep them in our (ever changing) diets. There’s always room for Mac & Cheese. GREG Reply · 24 October, 2014

5 from 2 votes (2 ratings without comment)

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