Mini Zucchini Millet Muffins (Gluten and Dairy Free)

These savory muffins use millet flour and are flecked with zucchini and lightly spiced with cinnamon and nutmeg, Mild and cute in mini form, these are a new favorite with my four year old.

It can be challenging to eat gluten and dairy free. It can be even more challenging when you are restricted beyond simply gluten and dairy free to sugar and fruit free too. But, thankfully, with a little experimentation, you can still eat quite well.

These muffins are an example of my experimenting so that my four year old can eat well while on a special diet to help with some candida issues. They are simple to make (a plus for the cook in the family), and tasty so that the whole family enjoys them, not just the special diet person.

They passed the test of my four year old, and my husband and I thought that they were tasty even without any added sweetener. They are perfect for dipping into stews or soups, or slathering with butter to eat hot out of the oven. Because they aren’t overly sweet, you can use them in a wide variety of contexts.

If you use a coconut oil that is sweeter to taste, it will give a hint of sweetness to the muffins that is quite nice. I used the coconut oil from Mountain Rose Herbs. They are far nicer than most gluten free products we’ve tried despite the fact that they aren’t full of sugar and various flours. These muffins only contain millet flour.

One note about millet flour. I love how light and neutral millet flour is, but occasionally I will have a recipe using millet that turns out with a funny taste and a burning in the back of the throat after eating it. It’s really strange. We’ve concluded that it must have to do with how old the millet is. While it didn’t smell or taste rancid, my older millet that I’ve milled had that effect, but this new millet I bought is mild and tasty.

These muffins are a little more dry than normal muffins, but not necessarily in an unpleasant way. Think cornbread, slightly crumbly, slightly dry, but in a good way. I choose not to use a type of milk in this recipe, but you certainly could. It would also make it a little more moist.

Mini Zucchini Millet Muffins

Yield: 16-20 muffins
As always, this recipe contains an overnight soak for better nutrition and texture.
The night before mix up the following:

    2 cups of millet flour (preferably freshly ground )
    1 tablespoon chia seeds
    3/4 cup of warm water
    1 tablespoon raw apple cider vinegar (you can substitute well fermented kombucha, water kefir, whey, coconut kefir)

Leave covered in a warm place for 12-24 hours. Preheat the oven to 425F and line a mini muffin pan with baking cups. Then add the following to the bowl.

    2 eggs, lightly beaten
    1 heaping cup of grated zucchini
    1 teaspoon salt
    1 teaspoon baking soda
    1 teaspoon ground cinnamon
    1/3 cup of coconut oil, melted gently
    1/4-1/2 teaspoon nutmeg (freshly grated is nice)

Whisk to combine and then fill muffin pans 3/4 full. Cook for ten minutes, or until a toothpick comes out clean when poked in the middle of the muffin. Remove from oven and serve right away with slivers of soft butter. Leftovers will last a few days in an airtight container.

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I love beautiful and simple food that is nourishing to the body and the soul. I wrote Fresh: Nourishing Salads for All Seasons and Ladled: Nourishing Soups for All Seasons as another outlet of sharing this love of mine. I also love sharing practical tips on how to make a real food diet work on a real life budget. Find me online elsewhere by clicking on the icons below!


  1. Valerie Josephson says

    thank you for this recipe! it’s so timely as just this week we have had to cut gluten and dairy products out of our 6y.o. daughter’s diet. I would love more ideas for things like this. I’m mostly concerned about getting enough healthy fats and also having something that looks appealing and tastes good in her lunchbox and for snack time at school while all the other kids eat cookies and pretzels.

  2. Amy Best says

    Wow, I think these may be Body Ecology Diet friendly! Of course I can’t have the eggs… any idea how they would do without eggs?

    • KimiHarris says

      Hi Amy!

      They are basically body ecology friendly muffins. 🙂 The eggs both add moisture as well as helping hold the muffins together. You could try adding more chia seeds to make up for the lack of eggs. They just might not rise as well without the eggs. Worth a try, though!

  3. Amy Best says

    Wow, I think these may be Body Ecology Diet friendly! Of course I can’t have the eggs… any idea how they would do without eggs?

  4. Rachel says

    These sound wonderful! I have had the same issue with millet tasting funny so I am a little nervous to try again. Do you have any good websites where I can learn symptoms, etc. of candida? I have a 3 yr old who may benefit
    Thanks for all you do!!!

    • KimiHarris says


      The body ecology has a “quiz” page that may be helpful to you. ( I find it interesting that you also had the same problem with millet. I’ve made several batches of millet muffins and no issues yet with this new bag of millet. I am assuming it happens with the millet is older, but I could be wrong!

      • Rachel says

        Thank you thank you! I am going to do that now!
        I know, the millet is weird. This inspires me to try again though!
        God Bless!!!

      • Rachel says

        Thank you thank you! I am going to do that now!
        I know, the millet is weird. This inspires me to try again though!
        God Bless!!!

  5. says

    They look really cute! I have used millet as a corn substitute for my corn sensitive daughter and love it – I even made a good “corn” bread with almond flour and millet! For those asking questions about replacing eggs, I would not recommend trying to use all chia gel. You end up with gooey little rocks. Ask me how I know… I would say use applesauce (¼c per egg) and a little xanthan gum, or a gelatin/water mixture. (Dissolve 1 tablespoon unflavored gelatin in 1 tablespoon cold water, then add 2 tablespoons boiling water. Beat vigorously until frothy.)

    • KimiHarris says

      Hi Hobby Baker,

      Thanks for sharing your experience with chia gel. I have been able to use all chia gel in wheat products to replace eggs and it went okay, however they were more dense. For my friend Amy, they would no longer be BED safe with applesauce added to it (though I think applesauce in gluten free recipes works great for added moisture!), but the gelatin and water idea is a good idea! Do you use the amount you called for above for one egg?

      • says

        Yes, that is for one egg, though I have seen less concentrated gelatin subs for eggs as well. I had another thought – when we had to go egg free for a while I actually used a flax meal based homemade mayo as an awesome egg subsitute for a cake. I remember omitting the cayenne and mustard since it was for a cake, but it turned out amazingly like real mayo considering it was egg free.

          • Amy Best says

            Okay, so I tried it today with the gelatin substitution for eggs. It worked well! How wonderful to find such a recipe! They are definitely fairly dry, any ideas for making them more moist? Possibly using homemade hempmilk instead of water? Even though a bit dry, they were still great. My kids loved them too. I was very impressed by the taste, even though no sweetener was used!

          • Amy Best says

            Oh, and I made regular sized muffins, worked great! And the gelatin I used was beef gelatin, I don’t know if that was the kind Hobby Baker used.

  6. Liz says

    I just made these muffins this morning and they are AMAZINGLY GOOD! I wasn’t sure how they would go over with my family, but I have 50lb of millet to make use of and lots of zuchs so I thought “what the heck?” What a delight! I used a regular sized muffin tin and baked a little longer at 400, and I had to substitute ground flax for the chia since I ran out. I am so grateful and pleased! Thank you!

    • KimiHarris says

      First, thanks for sharing that it worked with regular sized muffins. That’s good to know. 🙂 And so glad that you liked it!

  7. Amy Best says

    Okay, so I want to make these but was unable to get zucchini. What would they be like without? Or what else could you substitute? could you do grated carrot?

  8. Karin says

    Yum! I didn’t have nutmeg so just added more cinnamon. Excellent recipe! Next time I may add crumbled bacon for an even more savory snack. Id love to add some carrots too, and maybe raisins. Thanks these will be a staple in our house!

    • samara says

      Karin, you shouldn’t have mentioned bacon…that made me think of one of my favorite muffin recipes: A pear/cheddar muffin…hmmm…

  9. Kim says

    I absolutely love these (and so does my son). I am wondering about a couple things though. When soaking the millet flour, 3/4 c. water with the cider vinegar and chia seeds makes a really dry mixture… I had to quite a bit more water each time I made this. Then after soaking for 12-24 hours (covered) the mixture is almost hard. And the other thing I am wondering is your yield is 16-20 mini muffins. This yielded approx. 36 for me.

  10. Kim says

    We’ve often used grated raw squash, pumpkin or other vegetables as substitution for zucchini but we just discovered a very strange one this year: green tomato puree! We’ve had tomatoes continue to flower this winter (we live in the desert) but the tomatoes aren’t ripening b/c the sun is too low and the days too short. What to do with all those green tomatoes? Web research suggested pureeing and using in zuke bread–it was the moistest, best tasting we’d ever had! (And it was gluten free)

    We make millet muffins and bread in a square cake pan using red palm oil so it’s a beautiful yellow color. Everyone thinks it’s cornbread when we bring it to potlucks and gatherings!

    YES, millet must be ground fresh. When we grind too much for porridge and store the extra flour in fridge it is BITTER the next time we try to make it. Must go rancid easily…not sure why. We store it in the freezer now hoping that helps. It is very low in phytates so an overnight soak isn’t entirely necessary (as it is for oats which are very HIGH in phytates).

  11. Vanessa says

    I’ve not noticed a funny taste with millet, but have not, to date, enjoyed the texture millet meal gives. I’m hoping this recipe redeems millet meal for me. You mentioned a milk to make them more moist. Which ingredient would you switch for milk and would you use same quantities? Thanks, Vanessa

  12. says

    Thanks for this recipe. I made them today with grated carrot instead of zucchini and they were yummy. I doubled the amount of water for the overnight soak and they weren’t dry at all.

  13. Stephanie says

    I just made these and loved them! I doubled the soaking water as well and they are nice and moist. I also used pumpkin pie spice instead of nutmeg and sprinkled a little cinnamon on top. Yum!

  14. Heather says

    I made these and loved them, thanks! The only issue was that they stuck to the muffin cases. Should I make them without cases? Anyone else had this problem? I made regular size and minis and they both had 1/3 of the muffin stuck to the paper. Suggetions?

  15. Heather says

    I should also add that I took Stephanie’s advice and doubled the soaking water and used pumpkin pie spice instead of nutmeg. They weren’t dry, they were nice and moist, but stuck to the muffin cases. Hoping someone has some suggestions as I really loved these!

  16. Sarah says

    I’m so happy I found a muffin recipe that didn’t use any sweeteners! We’re doing baby-led weaning and I was looking for a way to introduce whole grains to my 8 month old. I made a few modifications because he can’t eat eggs and I didn’t have time to soak the grains overnight: used a mix of millet, whole wheat, and white flour, breastmilk instead of the chia seeds/water/vinegar, 4 Tbsp of applesauce instead of egg, kept the rest the same. I greased my muffin pan and didn’t use muffin cups – no problem with sticking. Next time, I may try straight millet, but the package scared me off (said it was good for “flatbreads”). I’ve never used millet flour before and wasn’t sure if it would rise without the wheat flour given the lack of egg.

  17. Daphne says

    I want to try this recipe but am wondering if I can use flax seeds instead of the Chia as it seems a lot of recipes say you can use either. I have never used Chia seed.
    Has anyone tried the pre-made ENER-G egg substitute for the egg, we can’t have egg. I may just try the applesauce, have baked many times with applesauce and it always works and adds sweetness.
    Thanks. daphne

  18. Luda says

    I made these muffins with adding 1/3c sugar which i could not taste much, for those who would like these on a sweeter side i would add cranberries or raisins other than that, im surprised how moist they came out with butter and little honey on top they were great fresh baked for breakfast =)

  19. Danna says

    I just put 24 mini muffins in the oven… I still have 3/4 of the batter left. It was rock hard last night when i mixed the flour and water so I doubled the water since I read in the comments that others did as well. Really curious to see how these turns out as I will have over 60 muffins

  20. Tara says

    I know this is an older recipe, but I’m wondering if you might see this comment and be able to answer. I have purchased some sprouted millet flour. Would I be able to use it in the same quantity listed in the recipe, and keep the liquid amount the same? Or would it need to be modified if I plan to use the millet flour *instead of* doing the soaking?

  21. shirley says

    Can I add some sugar to the millet zucchini muffins and how much. Husband does not like it without sugar.


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