Chili Cheese Muffins


This easy gluten-free muffin recipe is made with 6 healthy ingredients and can be whipped up in a jiffy. To make my Chili Cheese Muffins you’ll need almond flour, cheddar cheese, red pepper flakes, eggs, salt, and baking soda. Really, making this savory muffin recipe is that easy!

If you’ve been here before, you know that my specialty is easy grain-free recipes. I went gluten-free in 1998 when I was diagnosed with celiac disease. Because I still didn’t feel very well on a gluten-free diet, I took things up a notch and eliminated grains entirely in 2001. So, I’ve been writing grain-free recipes for quite some time. And these days, I love writing low-carb, keto recipes like this one.

Over the years, I’ve also worked quite a bit at keeping the ingredient lists in my recipes as short as possible. It’s a personal challenge for me, and a gift to you my readers, to save you all time in the kitchen, so you can get out and play.

On that note, I’m going out for a hike. Enjoy these quick and easy muffins my loves!

Print Recipe
  1. In a food processor, combined almond flour, salt, and baking soda
  2. Pulse in eggs, until well combined
  3. Briefly pulse in 1 tablespoon red pepper flakes, and cheddar cheese
  4. Scoop a heaping ¼ cup of batter into each paper lined muffin cup
  5. Top muffins with remaining 1 tablespoon red pepper flakes
  6. Bake at 350°F for 25-30 minutes
  7. Cool 1 hour
  8. Serve

If you are in need of low-carb breakfast ideas, try these Chili Cheese muffins with a side of eggs. If you’re grain-free, try these easy paleo breakfast recipes:

By the way, if you’re in need of nut-free paleo breakfast recipes, the Chocolate Donuts and Paleo Crepe recipes above do not contain any nuts!

March Muffin Madness

This post is part of March Muffin Madness, a round up of muffin recipes put together by my dear friend Shirley, from Gluten-Free Easily. Shirley is a pioneer in the gluten-free blogging world, and if you don’t yet know of her, you’re missing out! Shirley is a beekeeper, motorcycle rider, and has also lead support groups for those going gluten-free. Those are just a couple of the amazing things about her! Every year Shirley runs March Muffin Madness and I absolutely love being a part of it, and coming up with my own creative grain-free muffin recipe.

There is no Nutrition Label for this recipe yet.


114 responses to “Chili Cheese Muffins”

  1. Love all your recipes!
    However….. Can you put a weight alongside the cup measurements? We don’t use cups over here so I have to make up a recipe and weigh everything to get the macros…..sadly, sometimes a recipes has more carbs than I eat and I can’t enjoy it!

  2. These are great! I baked some for our anniversary dinner tonight. I made a few changes:

    I cut down on the red pepper flakes, and I added diced roasted chile peppers (hello, hatch chile season). I also threw in some garlic powder, smoked paprika, and cumin.

    My husband recently decided to Limit his grain intake (I’ve been limiting grains for over a year now). These will definitely help him with the big transition. :) Thanks!

  3. These came out great! Ran out of Honeyville, so half Honeyville and half Bob’s Red Mill. Also used Dubliner cheese. These might be the new go-to recipe. Thanks, Elana!!

  4. Elana, these are absolutely wonderful! For the people who are saying they are too spicy, I would suggest leaving off the chili pepper topping. That’s what we did for our 6 year old…we left a few ungarnished. My husband and I enjoyed the chili-topped version.

    I recently started eating wheat free after reading the book Wheat Belly, and these muffins are perfect for that lifestyle. I have PCOS, so I am hoping that eliminating wheat will help with some of my symptoms. Are you testing any more recipes for your blog? I noticed you haven’t posted in over a month…creating a new cookbook, maybe? :) I check your site every day in anticipation for your next wheat free recipe. Thanks for this recipe and for all of your hard work!

  5. Hi Elana,

    Just made the muffins and they are delicious!
    Are they freeze able, I don’t want them to go to waste?

  6. Elana, I just ordered your Paleo cookbook from Amazon. I am curious what you usually have for breakfast?


  7. Hi Elana, you have inspired me to start making my own grain/gluten free foods. I was diagnosed with celiac disease 3 yrs ago and still struggling with bloating and being overweight despite being gluten free. I am wanting to purchase a food processor or mixer to make my own bread and wanted your input on what brand you are using now? Thanks so much!

    • Hi Jennifer, thanks for your question. If you click the green text in the first line of the instructions for the recipe you will be taken to the food processor I have. BTW, I use it for just about everything and I don’t own a stand mixer :-)

  8. Elana, thank you for sharing your gift with us. I am grateful that you take the time to experiment and post what works. I have been grain free for about a year and a half now; and this grain-free world is easier to navigate with people like you helping us along the way. There’s not a recipe of yours that I’ve tried and did not like. They’ve all been amazing and performed just as you described. I really love your site and am always awaiting patiently for the next yummy delight. I made these chili cheese muffins twice already and the second time tonight I shredded and used a New Zealand cheddar and a Gruyere cheese. These muffins are absolutely to die for. I do not want to share them; am I selfish or what?

    • Hi Irma, you’re very welcome! So glad that you are enjoying these muffins as well as my other recipes :-)

  9. can i substitute the almond flour with apricot seed flour?
    i recived some flour substitutes from my amunt (grape seed flour, apricot seed flour, buckwheat flour) and i’m clueless how i can use them :)) these muffins look delicious <3

Have Something to Add?

Your comment will need to be approved before it will appear on the site.