paleo lemon poppyseed muffin

Paleo Lemon Poppyseed Muffins

Perfect Paleo Lemon Poppy Seed Muffins; made with coconut flour, they’re nut-free, and flavored with healthy lemon zest.

Who doesn’t love a good lemon poppyseed muffin? Now you can have Paleo Lemon Poppyseed Muffins that love you back. Made with coconut flour (for the nut-free folks out there) and a touch of honey, these quick and easy muffins are perfect for a brunch, potluck, after school snack, or a wonderfully summery dessert.

My boys and their friends devour these bite-sized mini-muffins and have no clue that they’re a gluten-free, grain-free dessert. I hope you enjoy these little Paleo treats as much as we do.

Print Recipe
Paleo Lemon Poppyseed Muffins
  1. In a food processor, pulse together coconut flour, salt, and baking soda
  2. Pulse in eggs, honey, shortening, lemon zest, and poppy seeds
  3. Spoon batter 1 tablespoon at a time into paper lined mini muffin cups
  4. Bake at 350° for 8-12 minutes
  5. Cool 1 hour
  6. Serve

I’m very excited that my new book, Paleo Cooking from Elana’s Pantry, comes out in less than one month, on June 18th. If you buy the book now you save over $4.00 off the list price.

Here are some grain-free muffin recipes from other bloggers:


  1. Linda Bennett-Cross says

    Just pulled out of the oven, one pan lemon poppyseed and one pan banana walnut muffins!😊 My caregiver did all the work while delt with the recipe. The first time baking for me since last Thanksgiving(2015> Thank-you very much, Can’t wait to try . more of your recipes!
    Linda from Vancouver, Washington, USA

  2. Debra Zantman says

    Hi Elana,
    I am new to your website and have read through some of your recipes. My husband was recently diagnosed with RA and his doctor said, get rid of all wheat. So we have been wheat free for 20 whole days. After reading Wheat Belly, i decided to become gluten free also and have been sharing that with friends. I have made your poppy seed muffins for the first time today and they are very good. I never would eat to many muffins before but it just sounded good. I am a vegeterian and have already had the mindset to eat low fat, well using coconut oils and nut oils is new to me, but i understand they are good oils. Eat Fat, stay thin, kinda idea. A idea i am still getting use to. I loved putting honey in these muffins instead of sugar or stevia. I have baked with Stevia and its just not the same imho. I will be relying on your website to new recipes as i have been learning to live wheat free. Thank You, you are appreciated…

  3. Jacy says

    Wondering if you have any recommendations on how to avoid honey? The only sweetener I’m currently allowed to eat is stevia, so if you have any ideas on how to remove the honey and what to sub, I would love to hear them! I was thinking maybe just increase the stevia and add some greek yogurt? Thanks!

    • Elana says

      Hi Jacy, thanks for your comment. I haven’t had success in removing the honey from my recipes. If you do experiment, please let us know if it works for you. In the meantime, here’s a link to my keto recipes, which do not contain any honey:


  4. Kat says

    I made this and the crumb is just perfect.I doubled the recipe but accidentally left the fat,honey,lemon zest and poppy seeds the one recipe measure, and used 5 eggs plus juice of a lemon. not too sweet and just buttery enough. next time I will use another T or more zest for more tang. Almost like a real wheat cake texture!!!

  5. Melissa says

    I dont have a food processor or shortning…has anyone had success with coconut oil and a wooden spoon? If so did u melt oul first (as i usually do when baking)

  6. Audrey says

    Hi Elana

    Could I double this recipe without interfering with the mixture ratios too much? Sometimes doubling doesn’t have a good result on some recipes.


  7. Leslie says

    I just made these with the following substitutions:
    Coconut palm sugar with a tablespoon of water replacing the honey
    1/2 teaspoon lemon essential oil replacing the lemon zest.

    A little dry still and not lemony enough. Will try again for sure. Still good flavor!

  8. Elanore says

    I am ten years old and paleo and I love baking.I have been looking for a good paleo poppy seed muffin for a long time and these are by far one of my favorite recipes of all time.I cant wait to try them!:)

  9. kellyrae says

    I made these this morning. I kept looking in the bottom of the bowl at the 1/4 cup of flour thinking how on earth is that going to make 20 mini muffins!!! I reread the ingredient list about 6 times thinking you must have forgotten a 2 in front! I persevered. I substituted coconut oil for the palm shortening as I don’t think we have palm shortening here in New Zealand, but I am no baker. I used regular salt as its all I had.
    It made 9 x 2inch high muffins (very very mini), I had to bake them for 25 minutes. They looked pretty darn good when I pulled them out of the oven. THEY WERE DELICIOUS! My 11 year old son and my husband were suitably impressed and I am so happy as it is the first thing I have ever baked gluten free that has not gone straight into the bin! Thank you. I am so looking forward to your other recipes that I have printed off, and your books are coming to me soon in the mail!

  10. Sarah says

    I used melted butter in place of palm oil and the muffins came out fine. This was the first coconut flour recipe for me that actually turned out light and airy, sort of cake-like. I will definitely make these again. Next time, though, I will add a tsp or so of fresh lemon juice, as I thought, even with the T of zest, I’d like more lemon flavor. Also, I barely eeked out 12 mini muffins with the above proportions–hopefully doubling the recipe will work out and yield more muffins.

    • Elanore says

      I used melted butter and they turned out great to. I also made regular size muffins and greased the tins with coconut oil instead of paper liners.I know, I’m a rebel.

  11. Vallery Rogers says

    I just found the recipe for Paleo Lemon poppyseed muffins, but didn’t see the calorie or carb or protein content. Is that in the book?

  12. CPW says

    Thank you for this recipe! These are delicious! I didn’t have a mini muffin tin, so I made 5 mini bundt cakes instead. Cooked them for ~20 minutes. So good! Next time I think I’ll double the recipe!

  13. says

    I was feeling under the weather last night and was craving some kind of comfort food, so I made these. They TOTALLY hit the spot and I felt better afterward (plus I had left overs for breakfast this morning). THANKS!

  14. Teri F says

    I wonder whether these could be made substituting something for the sugar/honey. Swerve? but mine is a powder, which will change the consistency.

  15. Pamela says

    Just made these using butter and just a 1/2 tsp of pure stevia instead of honey. My boys are in heaven. Thank you for sharing.

  16. Andrina says

    These are in the oven now and smell amazing. At 8-12 min they look wet still . Should they cook like normal and come out clean on a tooth pick ?

  17. Cindy says

    Hey! Do you need the honey? I’m on a no added sugar kick right now. Do you need it for consistency? Any ideas on other options? I could do unsweetened applesauce or bananas (since I’m allowed fruit but not eating much of it).

  18. says

    Hi Elana!

    I made these with coconut oil instead of shortening, raspberries instead of poppy seeds, and 1 egg + 2 egg’s worth of egg whites. They came out a little flat, lumpy, a little greasy, stuck to the liners, and were a little wet. The boys liked them but I wouldn’t really say they were awesome.

    I am thinking the wetness of the coconut oil and weight of the raspberries were my issues. Maybe by reducing the amount of coconut oil or subbing half of the honey for something like stevia (reduce wetness) would work? If anyone tries that, let me know! :-)

  19. Michelle says

    I use coconut oil, it works well. I also mix these in a mixing bowl and add 2 tbsp of lemon zest instead of 1. I’m going to try it with butter today as the coconut oil is a little greasy. These are delicious!

  20. Justine says

    I just made the, double batch in a normal size muffin pan..Made 11 muffins baked at 350 for 17 minutes and of course they were absolutely PERFECT, as every of your other recepies! THank you Elana!

  21. Rachel says

    I made these muffins last week and we loved them! My oldest son (who called them “lemon mommy puffins” when he was young) requested a lemon poppy cake for his 12th birthday yesterday, so I doubled the recipe and cooked it in a pie pan. His 8 year old brother made a glaze with coconut oil, honey, and cream. It was soooo good!

  22. BubbyMC says

    When using coconut oil do you measure it when solid or liquid? I have found that 1/4 cup of solid coconut oil is much more than 1/4 cup when melted.

  23. miche says

    These we’re great! We ate the whole tray. Next time I would use a bit more lemon for more zing! I also used a regular muffin tin and got 6 total. I would double up if your making the regular size. The mini is too small for me. Thanks!

  24. Mia says

    I cannot wait to make these! I have all ingredients on hand and I know there are going to be devoured:)
    Also excited to get the new book. Thank you for making it so affordable!

  25. says

    I just made these and they turned out great. I doubled the batch, used coconut oil instead of shortening, maple syrup instead of honey and grated an entire large lemon instead of measuring (with 6 eggs, I was afraid it would turn out too eggy tasting). I also added blueberries and made these in regular sized muffin tins. They took longer to cook but turned out moist and flavor full.

  26. Emily says

    I just found out our son has an allergy to eggs, along with a bunch of other things. I’ve been baking gluten free for a long time and enjoy the use of coconut flour, however my understanding is that eggs are a must. Is there a good substitute for eggs when using coconut flour?

  27. Eva says

    These muffins are wonderful and super easy to make! I used coconut oil and will definitely make them again!

  28. Patty says

    I just made these … In a bowl … With coconut oil … In regular muffin tins … Added blueberries. Hah! I could not fathom that only 1/4 cup of flour would work. I added in the equal amount if almond flour, too. All good.

    • Michelle says

      Try Brown Rice Syrup, same sweetness, stickiness and consistency as honey. I use as a Honey/Sugar substitute in most recipes with no difference in results :)

    • Kate says

      I love coconut nectar by Coconut Secret and it is vegan with a low glycemic index too, you can find it at most health foods stores like Whole Foods,

    • JMB says

      Rice Malt Syrup – ‘Pure Harvest’ is the brand I buy in Australia (from the health food section of Coles). Has the added advantage of being fructose free which is why I use it. It is similar to honey in colour and texture but is not as sweet.

  29. Harshi says

    I would love to try these yummy muffins. But what can I use instead of shortening? I’ve got coconut oil. It’s hard as its cold here now.


  30. says

    Thanks for linking to my Paleo-style muffins, Elana! So far, I’m loving almond flour but I remain too chicken to work with coconut flour – even though I have a bunch in my pantry. Maybe your lemon poppyseed muffins are the place to start.

    xo Nicole

  31. Jennifer says

    Hello Elana,
    Would this recipe work if I mixed it in a bowl? Or is the food processor necessary?
    Thank you for making such delicious gluten free recipes! My 10 year old g-free kid gobbles up lots of treats thanks to you. I’m so glad that you’re using coconut flour. Are their more coconut flour recipes in your new cook book?
    Thanks, Jennifer

    • Jennifer says

      I can’t see why a bowl wouldn’t work. I have made similar recipes using wooden spoon power only :). I’d suggest missing the dry ingredients in one bowl, the wet stuff in another, and then stirring them together.

  32. Deb M says

    I have the same question as two others – about substitutions for vegan shortening. I am interested in using coconut oil, avocado oil, or olive oil for a substitute. I was also thinking that a combination of olive oil and applesauce might work. Does have anyone have a thought on good substitutions?

  33. says

    Oh, Elana, I love these muffins! Can’t wait to give them a try! Maybe even this weekend. It’s unseasonably cool and the house could use some warming up. ;-) I can’t think of a better reason to do so and a better reward for turning on the oven. Thanks, dear!


  34. Deb says

    This recipe looks great – can’t wait to try it! Any chance of substituting coconut oil for vegan shortening? Thanks!!

    • Rachel says

      I just tried substituting coconut oil for the same quantity of shortening. I stuck it in the fridge for a bit before adding it to the food processor. The muffins were a hit! They’re pretty greasy on the bottom, but I often find that with coconut oil. It certainly didn’t stop them from being gobbled up, that’s for sure.

  35. Lydia says

    Another delicious-looking recipe, Elana – Thank you!

    FYI, I’ve been toying with substituting almond flour for all or part of the coconut flour, or vice versa, in some recipes, and I’ve come up with a fairly reliable ratio for baking performance. Basically, 1 gram of coconut flour is roughly equal to 5 grams of almond flour in baking, all other ingredients/amounts remaining the same. It’s not foolproof, but if you’re a pretty confident baker and patient enough to test it on familiar recipes, it’s a good starting point. I’ve tested it on a few recipes with good results.

  36. Kristen says

    Coconut flour and lemon… yum! I’m always on the lookout for good coconut flour recipes. Can’t wait to try these! :)

      • says

        A good substitute here would be butter or expeller pressed coconut oil or ghee. I have used these all interchangeably with organic palm oil with good success in Elana’s recipes. Extra Virgin Coconut Oil is good but it would impart a coconut flavor to the recipe.

        • says

          I can confirm butter works fine as well if you don’t want to use the shortening. Still tastes incredible, really grateful for this recipe too :)

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