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Paleo Lemon Poppy Seed Mini Muffins :: Gluten/Grain Free, Dairy Free, Nut Free, & Refined Sugar Free!

March 24, 2018

Healthy paleo lemon poppy seed muffins are your answer from everything to Easter brunch to your weekday school morning breakfast rotation!

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Signs of spring!

I saw my first robin of the spring last week, and while that might not seem like huge news, it pure joy after bitter cold and snow for the last 4 months! We are perfectly giddy to put the snow gear away, and have been enjoying more daylight, sunshine, and the promise of warmer air coming soon! I hope you are seeing signs of spring where you live too.

Easter brunches memories

Lemon poppy seed muffins are about as spring as it gets! I remember the little lemon muffins piled up across brunch buffets for Easter years back, and was always drawn to the bright, fun flavor. I don’t know why it never dawned on me to try to make them myself, but I have been having so much fun testing the idea of these little mini bites in a healthier way, and my girls have fallen in love with the idea as well.

Best of both worlds

Let’s face it…sometimes gluten/grain free baked goods just aren’t the same. They can turn out dry and crumbly – we have all been there. After over a decade of baking gluten free with years scattered in there that had to be grain free, I will be the first one to admit it takes some practice. You will love how soft and fluffy these lemon poppy seed muffins feel though! I am always blown away when I work with cassava flour – when you do it right it really has a great, soft, gluten-like texture. And of course you can’t go wrong with lemon and honey for the flavor! I think my favorite part is the hint of almond extract that really takes it over the top.

Quick and easy batter *and* freeze-able…yes please!

Because these mini lemon muffins are not only perfect for the Easter brunch! They pack perfectly for your hiking adventures, and be a great addition to your weekly school morning breakfast rotation too. The batter blends right up into a 4-cup measuring cup to pour right into your muffin pan, and can be blended up ready to go in less than 10 minutes! I did my freezer test on the muffins last week, and the texture holds up as well as taste. Bulk up and make your mornings easier!

How to make lemon poppy seed muffins a school morning breakfast

Because it is what I do best…let’s get practical 😉 Easter brunch is great, but these muffins are so great for a quick school morning breakfast too. Here are some ways to make it a balanced meal for your kiddos:

  • Lemon muffins and glass of raw milk/coconut milk (You can pack the milk in a thermos if on the go. I used these for travel drinking for my little ones). You can spread butter on the muffins too.
  • Lemon muffins spread with coconut butter, and dish of coconut yogurt. You can add collagen to the yogurt for extra protein too. If doing this to-go, just put the yogurt in a to-go container.
  • Lemon muffins with breakfast meat and a banana. (Bacon, sausage, or even dinner leftovers like chicken or beef – I served my kids meat leftover from dinner for breakfast since infanthood so they really don’t know any differently. If you have little guys at home, start now – it makes life so much easier down the road!)
  • Lemon muffins, raw cheese/goat cheese, and grassfed beef jerky make a great on the go bowl of little bites!
  • Lemon muffins, cubes of avocado, a few almonds, and a clementine make a great on the go bowl of little bites too!

Don’t forget the lunchboxes!

The girls have loved having the lemon poppy seed muffins in their lunchboxes to go with a thermos of soup, or in their morning snack container for mid-morning. It is a great boost of energy that isn’t full of sugar and has blood sugar stabilizing protein, fat, and fiber in a balanced combination.

Ingredient notes

  • Make sure to measure out the lemon juice – my lemons may be more, or less juicy than yours, and the liquid makes a difference in the final product.
  • You can swap the sweetener for your choice. We get a local raw honey from a farmer we love and the taste is so amazing. Just be sure to pick a honey that you love the taste of. If you get a very flowery honey, your muffins will take that taste on (which might be a good thing if you like that!). If you don’t have access to a quality raw honey, this is a good brand. I think coconut sugar or pure maple syrup would swap well too – the honey goes with the lemons so well though.
  • You can swap the coconut milk for raw milk/cream if you tolerate dairy. I don’t think rice milk will be fatty enough. Cashew or almond milk/cream should be fine. I do not recommend consuming soy milk.
  • I have not tried other swaps for the cassava flour. Even if you are not grain/gluten free, I would recommend giving your guts a break from the typical flours you use and try something new! Cassava flour is made from the cassava plant which is a root vegetable. It has numerous health benefits from gut flora feeding PRE-biotic fiber and healthy, energy giving carbohydrates.
  • Egg free friends, I think you could make a few flax eggs to swap here. I would add a splash of ACV to help react with the baking soda to help with some rise – the muffins might not puff up as much as these since eggs really help with rising, but I know they will bind well and should taste great. I have made these with duck eggs if you happen to tolerate those better (my daughter and I tolerate duck eggs better than chicken eggs). If you try an egg free alternative, please let us know how it turns out in the comments so that other egg free readers might gain from your experience. Thank you!
  • I think you could leave out the collagen if you don’t have access to that. I love the extra bit of protein and gut nourishment it provides, and collagen tends to lend some softness to baked goods that I love.

Little hands friendly, and toddler approved!

I’ve been a bit laid up over the last 6 weeks healing a broken wrist (boo!), and I’m telling you, dear momma, I am so thankful for this mini muffin pan that I just happened to get not to long before that. I have been able to have a freezer bag filled with quick, healthy muffins for my littlest to munch on for early school mornings, and I can back off on too much breakfast cooking. Toss a few mini muffins in a little bowl with a hardboiled egg, and your little guy can have a nutritious breakfast on the way to dropping siblings off to school, or packed up in a container to have for breakfast at daycare.

Print Recipe
4.85 from 20 votes

Paleo Lemon Poppyseed Mini Muffins

Healthy paleo lemon poppy seed muffins are your answer from everything to Easter brunch to your weekday school morning breakfast rotation!
Prep Time5 minutes
Cook Time11 minutes
Total Time16 minutes
Course: Breakfast
Cuisine: American
Keyword: Paleo lemon poppyseed muffin recipe, Paleo lemon poppyseed muffins
Servings: 24 mini muffins
Author: Renee -


  • 3 eggs
  • ¼ cup raw honey This is mildly sweet - you can taste the batter and add more to taste if you like. I get raw honey from a local farmer. If you don't have access, THIS is a good brand.
  • 1/3 cup avocado oil Melted coconut oil or butter should work too
  • ¼ cup juice from a lemon this has been 1 medium/large lemon for me
  • 2 tsp almond extract Vanilla extract would be nice too if you can't have nuts or don't have almond extract around
  • 1/3 cup coconut milk
  • 1 cup cassava flour
  • ¼ cup grassfed collagen
  • ½ tsp baking soda
  • ¼ tsp sea salt
  • 1 heaping tbsp lemon zest this has been the zest of 1 lemon for me.
  • 1 tbsp poppyseeds optional if you don’t like them


  • Pre-heat the oven to 375 degrees and grease your mini muffin pan. I like to use this avocado oil spray for ease, but you could dip a paper towel in some avo oil to wipe the pan.
  • Blend the eggs, honey, oil, lemon juice, and almond extract for 1 minute on high. I have been making my batter right in my 4-cup liquid measuring cup to make for easy pouring right into the muffin pan – it fits perfectly. A small mixing bowl works too.
  • Add the coconut milk, cassava flour, collagen, baking soda, salt, lemon zest, and poppy seeds, and blend on low until combined.
  • Pour the batter into the greased muffin pan and bake at 375 for 11 minutes. Let the muffins cool in the pan for a few minutes before turning out onto a cooling rack to cool the rest of the way. To freeze the muffins, let them cool completely before putting into freezer safe bags.

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  • Reply linda spiker March 26, 2018 at 1:38 pm

    5 stars
    These look heavenly! I need to start baking!

  • Reply Lindsey Dietz March 26, 2018 at 2:52 pm

    5 stars
    Yep, yep, yep! I am in love with lemon poppyseed anything and especially when it’s in a convenient package like this! I always need new, easy breakfast ideas, and this one is great!

  • Reply Emily @ Recipes to Nourish March 26, 2018 at 3:00 pm

    5 stars
    I can’t wait to make these!!! I love that you used cassava flour and all that collagen. LOVE the lemon flavor too! So perfect for spring. Such sweet photos Renee, love seeing those little hands.

  • Reply Jean March 26, 2018 at 5:22 pm

    5 stars
    These are so perfect for spring! I’m in love any lemon flavored baked goods, so I’m sure I’ll love these.

  • Reply Holley @ March 26, 2018 at 7:48 pm

    5 stars
    I passionately love lemon cake and lemon muffins. These look so good!

  • Reply Tessa Simpson March 26, 2018 at 8:34 pm

    5 stars
    I am seriously drooling….these look AMAZING!! You have all sorts of lemon goodness coming our way lately!

  • Reply Joni Gomes March 27, 2018 at 9:30 am

    5 stars
    I was just working on a list of snacks to make for my husband while I’m out of town. Definitely making these for him (and maybe taking a couple for my travel).

  • Reply Megan Stevens March 27, 2018 at 10:10 am

    5 stars
    Such fun little bites — healthy cake, mmm! I really like your suggestion to serve these with goat cheese and beef jerky. That’s just how we do lunches around here, and I usually throw a little lettuce their way, too, because I got 2 boys who like greens! 😉 Thanks, Renee, for another fun baked good recipe!

  • Reply Christina Shoemaker March 27, 2018 at 11:16 am

    5 stars
    How adorable are these!! I bet they’re perfectly sweet and totally addictive too!

  • Reply Yvonne March 27, 2018 at 12:26 pm

    5 stars
    These muffins would be such a nice addition to my Easter brunch menu. I think my boys would gobble these down in a second.

  • Reply Yang March 27, 2018 at 2:41 pm

    5 stars
    These are the prettiest and cutest muffins and so easy to make! I can’t wait to try them 🙂

  • Reply Melissa @Real Nutritious Living March 27, 2018 at 4:34 pm

    These are so cute! I haven’t had poppy seed anything since I was a kid- so excited!

  • Reply Jessica DeMay March 27, 2018 at 10:13 pm

    5 stars
    These are so cute and I love how healthy they are! I know me and my toddler would love them!

  • Reply Monique March 28, 2018 at 12:16 am

    5 stars
    These muffins look so pretty and perfectly formed (haha, is that a weird thing to say?)! I love lemon in baking, it’s such a wonderful flavour!

  • Reply Jo Romero March 29, 2018 at 6:57 am

    Totally going to make a batch of these over Easter and put them in the freezer – so handy for packed lunches or snacks. Great recipe!

  • Reply Tina March 29, 2018 at 8:13 pm

    Loooove it! Sounds amazing – can’t wait to try!

  • Reply Carrie | Clean Eating Kitchen March 30, 2018 at 10:01 am

    5 stars
    These muffins look so light and fluffy! Perfect for a grab n go breakfast!

  • Reply ChihYu March 30, 2018 at 4:26 pm

    5 stars
    YUM! They look so flavorful and delicious ! Totally love it !

  • Reply STACEY CRAWFORD April 2, 2018 at 2:32 am

    5 stars
    Yay, I just adore lemony baked goods. These look fabulous. Your kids are so cute and love the heart shaped bowl 🙂

  • Reply Tatiana April 2, 2018 at 4:16 am

    Muffins look so cute and spongy! Perfect for little hands and for parents too.

  • Reply Katja April 2, 2018 at 3:04 pm

    5 stars
    These are just absolute perfection. I love lemon muffins. And I love that they are made with cassava flour. I’ve baking with it more and more.

  • Reply Becky Winkler April 9, 2018 at 11:02 am

    These are so cute, and the texture looks perfect!

  • Reply Michelle June 28, 2018 at 3:18 pm

    2 stars
    I really wanted to love these, but they came out super dense and gummy and not at all like the texture pictured =( The only sub I made was using half & half instead of coconut milk. Any suggestions??

    • Reply Renee Kohley June 28, 2018 at 6:04 pm

      Hi Michelle! I am not sure if the half and half is the difference but it really could be since it is a totally different make up than coconut milk. I make these every couple weeks and they turn out perfect each time! I’m sorry they didn’t work out for you!

  • Reply Kari - Get Inspired Everyday! July 30, 2018 at 9:50 am

    5 stars
    These look so good, I love lemon poppyseed muffins, but it’s been forever since I had one! So thanks for a great recipe!

  • Reply Nicole August 10, 2018 at 1:13 pm

    5 stars
    I just made these yesterday. They were AMAZING! Thank you for a delicious and nutritious snack on the go! I may have overfilled my mini muffin pan, so they weren’t the prettiest, but they tasted wonderful! This was my first go at GF baking. Thank you 🙂

    • Reply Renee Kohley August 14, 2018 at 8:59 am

      I’m so glad you enjoyed them Nicole! Thanks for coming back to let us know!

  • Reply Ann December 1, 2018 at 8:38 pm

    Has anyone tried these using standard muffin tins? What would be the change in baking temp/time?

    • Reply Renee Kohley December 8, 2018 at 10:37 am

      Hi Ann! I have done this once or twice and you just cook maybe 10 minutes longer.

  • Reply Emily February 28, 2019 at 9:00 pm

    Is there a substitute for collagen? I don’t have that on hand. Thank you!

    • Reply Renee Kohley March 5, 2019 at 12:31 pm

      Hi Emily! I think I would just leave the collagen out of the recipe then – it shouldn’t change the outcome 🙂

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  • Reply jackie grant June 9, 2020 at 9:35 am

    has anyone made these with an egg substitute?

  • Reply Jenessa August 22, 2021 at 9:44 pm

    Yum! I just wanted to say that using a gluten free flour in place of cassava worked well! I wish I had cassava, and respect the need for diet variety, but sometimes you just don’t have an ingredient but you want to make the recipe. So Bob’s 1-to-1 GF flour worked well!

    • Reply Renee Kohley August 23, 2021 at 1:51 pm

      Hi Jenessa! That is so good to know! I don’t always have cassava on hand either! Thank you for sharing!

  • Reply Stephanie November 9, 2021 at 10:39 pm

    I just made these today using flax eggs and a splash of acv like you suggested. They turned out beautifully!

    • Reply Renee Kohley November 10, 2021 at 8:54 am

      Hi Stephanie! I’m so glad you enjoyed the egg free version! Great! Thank you for sharing!

  • Reply Courtney November 10, 2021 at 6:14 am

    Hello! We are unable to get cassava flour where we live. Is there another option? Thanks!

    • Reply Renee Kohley November 10, 2021 at 8:56 am

      Hi Courtney! I think a combo of almond flour, coconut flour, and tapioca starch would give the best texture – can you use those? The batter should be like a thick pancake batter as you can see in the pictures above – you will have to play around with the amounts a little – cassava flour alone is super absorbent so you don’t need much of it to soak everything up – you may need to add more of the other flours, though keep in mind too much coconut flour can make things dry and crumbly. Let us know if you give them a try and what works for you!

  • Reply Rachel Free November 10, 2021 at 8:18 am

    These look amazing!! Can’t wait to try them!

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  • Reply Brittany November 18, 2022 at 10:07 am

    The texture of these are great! But sadly I couldn’t taste any lemon. Also please tell me your secret to get a heaping tablespoon of lemon zest from one lemon. I had to use 4!

  • Reply Erin January 21, 2023 at 10:09 am

    Made these today – they’re amazing!! The texture is perfect, and the flavor is spot on. Just the right amount of sweetness!

  • Reply Jasmine January 28, 2023 at 11:29 am

    I made these today and I agree they could’ve been more lemony. Also i had a really hard time coming up with a pourable battery. I added more eggs, coconut milk And even a touch more lemon, but it remains very thick. Finally i plopped spoonfuls into muffin mold. The family liked the flavor but I think I Projekt need to bake them a little longer next time. I wonder why it was so dry… maybe my flour was too dry? Is that a thing?

    • Reply Renee Kohley January 29, 2023 at 11:57 am

      Hi Jasmine – what brand of cassava flour did you use? Different brands absorb very differently. I only use Otto’s cassava flour, so in my recipes, it will work best with that brand.

  • Reply Jasmine January 28, 2023 at 11:34 am

    The only thing I can think of is that I weighed everything in grams bc i didn’t have measuring cups. Do you think this is what made the difference? For example 1 cup of cassava flour weighs 285g…

  • Reply Jasmine January 31, 2023 at 6:21 am

    We’re in Portugal so it’s definitely not Ottos!

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