Chili Cheese Muffins

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!

Chili Cheese Muffins
Serves: 9
  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. Garnish muffins with remaining 1 tablespoon red pepper flakes
  6. Bake at 350° 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.


  1. Lauran says

    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!

  2. Leslie says

    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!!

  3. Krissy says

    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!

  4. Lauren says

    Hi Elana,

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

  5. Marsha Gibbons says

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


  6. Jennifer Anne La Perna says

    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!

    • Elana says

      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 :-)

  7. Irma says

    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?

    • Elana says

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

  8. Imola says

    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

  9. Shirley @ gluten free easily (gfe) says

    Thanks so very much for both participating in and sponsoring March Muffin Madness, Elana! This is such a simple, yet terrific recipe–your trademark! I’m actually making these muffins tomorrow to go with a pot of soup for neighbor friends. I know they will love the combo. :-) The nine readers who won your cookbooks in MMM are all thrilled, of course. Thanks again on all, dear!


  10. Barbie says

    These are absolutely delicious! Love the texture and the flavor. I used very fresh chili pepper flakes in the full amount listed in the recipe and they were definitely hot… we loved them, but I can see that sometimes I might want use fewer flakes for a milder taste. I think they’d be tasty even without the flakes.

  11. Jennifer says

    Hi Elana, this looks fantastic, can’t wait to try it. I’ve been using your recipes for a few years now & have loved every single one of them. I found out recently that I have Ankilosing Spondylitis and then yesterday, it was confirmed that I most likely have MS too, so now I look @ your site daily, my family likes your recipes too! Thank you for all of the information you have provided, your site will be extremely helpful for many years to come. God bless you & your precious family!

  12. Vicki B. says

    I think they might be a bit spicy f o r my palate, but might try them with fewer pepper flakes. Excited about the giveaway!

  13. Karen says

    What a great recipe! I used rosemary instead of chili and Diaya Italian Blend shreds. Turned out great. Wondering if the batter would hold up as a biscuit. Definitely will make these again. Thanks for the great recipe.

  14. Tawni says

    My imagination is running a little wild with different herbs and spices I can use in these – instead of or in addition to the chili pepper. I love kitchen creativity!

  15. Megan says

    Well, it looks like I know what I’ll be doing this weekend! :) A big pot of chili with a side of these muffins! Thank you!

  16. christopher says

    your recipes are fantastic! the muffins look warm and inviting. they remind me of childhood chicken dinners with my family. everything i’ve made on your site has been a smashing success. thank you for your hard work and generosity!

    • Elana says

      Christopher, you’re welcome! Thanks for letting me know that everything you’ve made from my site has been a smashing success!!!

  17. Kerstin says

    I have made several of your recipes – always a big hit, so I am looking forward to making these. Thanks for your delicious recipes you share with us!

  18. MaryAnne says

    I’ve been thinking about buying a Kitchen Aid Mixer for mostly Baking recipes, but I notice you seem to use the Blender all the time now.. Can you briefly advise which is the best purchase since I can only buy one item to assist me with all my recipes.
    Thank you for your generous Support and sharing of information and recipes.

    • Elana says

      Hi MaryAnne, I don’t own a stand mixer so cannot advise regarding that type of purchase. I use a food processor (for this and many other recipes) and a Vitamix blender to make soups, smoothies, and nut milks. I would recommend purchasing each one used if you can find them online or at a yard sale. I hope this is helpful!

      • MaryAnne says

        Thank you for your prompt reply. I’m just wondering what the reason is that you do not own or use a Stand Mixer. Is there a big difference in how a mixer as opposed to a food processor work? Thank you in advance for your reply to this question.

        • Elana says

          You’re welcome MaryAnne! I am a minimalist and like to keep my kitchen counters and cabinets as clutter-free as possible. I have found that the food processor can do almost everything that a stand mixer does. So, that’s why I don’t own a stand mixer :-)

  19. Karen says

    These look great (sans the chili). I can’t do the spicy but…….I think I will try them with the Daiya pseudo cheese. I seldom do processed food but I’ve been jonesing for some savory muffins so I’ll give that a shot. These sound like they would be perfect with soup and a salad.

  20. Ania says

    Hi Elana, I have never seen almond flour where I live. What’s the difference between flour and meal. Sorry, you were probably asked this many times before.

  21. Carol Biggs says

    These Chili Cheese Muffins were so easy and delicious!!! My husband wanted to eat them all up in one sitting. Am going to send the recipe to 3 of my gluten-free friends.

  22. Laura says

    these look great! with a little spice even my non-paleo partner will eat them :) and would love to make these as a dinner roll/cornbread substitute. ideas on what to pair them with other than chili?

  23. Nancy Hildebrandt says

    Normally when a recipe for totally yummy muffins appears in my Inbox, my heart sinks. But wait, it’s from Elana! I know without scrutinizing the ingredients that I’m going to be able to eat it for sure! It’s going to taste great, be easy to make, and somehow magically be good for me at the same time! Thank you so much for your endless creativity with ingredients.

  24. Caroline says

    Can’t wait to try. Love the simplicity and the specificity. I just realized I have almond meal, not flour.

    • Elana says

      Caroline, thanks so much for your comment! I think being as clear as possible makes things easier for my readers :-)

  25. Denise Pearson says

    Hi Elana,

    I just wanted to thank you for starting this fantastic blog and for sharing your wonderful recipes and advice! You put in all the hard work experimenting and perfecting the recipes so we don’t have to go through the trial by fire :)

    Have a great day!

  26. Noelle Kelly says

    I might in fact make these muffins for dinner tonight! Thanks a bunch. Looks like a quick chili is in order for tonights dinner. Would go perfect with these. YUM! Thanks for the giveaway.

  27. Leize Day says

    This recipe sounds marvelous! I have made so many of your muffin recipes that I’ve lost count! Your Haman cookie recipe was also a big hit. Thanks for all your time and effort.

  28. Sheila says

    Heading to the health food store for almond flour and then making these cheesy muffins. Thanks for the amazing giveaway!!

  29. Greg says

    Spicy? Cheesy? Muffins? Yeah, you need to change the servings to “1” with me. These are not going to last. Thanks!

  30. Kim Kaiser says

    This muffins sound fantastic….a nice savory recipe that would go great as a side with your shepard’s pie recipe which my family loves.

  31. Jeetu Melwani says

    Thank you, thank you for all your wonderful recipes.I always include gluten free foods in my diet and this recipe is delicious .

  32. Becky Winkler (A Calculated Whisk) says

    A savory muffin–great idea! The texture looks perfect and I’m super impressed by the short ingredient list. Pinning to try soon!

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