Almond Flour Lemon Poppy Seed Muffins

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These paleo Almond Flour Lemon Poppy Seed Muffins have a light, fluffy texture and are BURSTING with fresh lemon flavor. They’re the perfect yummy breakfast or snack! (Gluten-Free & Dairy-Free!

almond flour lemon poppy seed muffins stacked next to a bottle of milk

We live in one of the sunniest states in the U.S., so we have VERY mild winters, but I always find that March feels like turning an energizing corner from winter to spring. In the kitchen, this means I only have a little longer to wait before berries are in season (my kids can’t WAIT), and we have the last of winter’s sunny citrus to send us off.

Lemon always tastes like sunshine to me, which is why I get the itch to make all things lemon this time of year! I’ve posted plenty of lemon recipes on this blog from soup to salad to cake, and today I’ve got a lemony breakfast that feels perfect for spring (or Easter brunch down the road): paleo Almond Flour Lemon Poppy Seed Muffins!

Packed with LOTS of bright lemon flavor and dotted with poppy seeds, these light, tender, fluffy muffins are made from better-for-you ingredients and taste incredible. Like, IN👏CRE👏DI👏BLE👏.

Preheat the oven and bust out the muffin pan! Here’s all you need to get started on this easy muffin recipe…

ingredients for almond flour lemon poppy seed muffins

Simple Ingredients To Start

  • LEMON ZEST + LEMON JUICE. To start off, these paleo lemon poppy seed muffins get a super-charged dose of lemon flavor with a combination of fresh lemon zest and fresh lemon juice.
  • AVOCADO OIL. I like avocado oil because it’s so neutral-tasting, but you can substitute another neutral oil, if you like.
  • EGGS. A few large eggs help bind the batter together and help give these paleo muffins their soft, springy texture.
  • (DAIRY-FREE) MILK. We’re dairy-free, so I use a dairy-free milk like almond milk, cashew milk, etc. You can use whatever your family drinks! The milk will also take on some acidity from the lemon juice, which adds a buttermilk effect here. The result is extra light, fluffy, tender muffins. Win-win!
  • MAPLE SYRUP OR HONEY. To keep these almond flour muffins naturally sweetened, I love using pure maple syrup or some good-quality honey. Both allow the lemon flavor to really shine!
  • VANILLA + LEMON EXTRACT (OPTIONAL). Vanilla extract adds another layer of sweetness and tastes lovely with the lemon. If you like your lemon muffins extra punchy (like I do!), I recommend adding the optional lemon extract. (You can also use 1 drop food grade lemon essential oil)
  • ALMOND FLOUR. You’re looking for finely ground blanched almond flour. The finer, the better! Almond flour is pretty moist and a little dense on its own, so I pair it with…
  • TAPIOCA STARCH OR ARROWROOT. You can use either of these starchy flours that keep the muffins light and fluffy and give them their soft, delicate crumb. I don’t recommend skipping it or substituting it with more almond flour, or your muffins will not rise and hold together as well. (Don’t have either of these? Cornstarch is your best substitute.)
  • BAKING POWDER + BAKING SODA + SALT. The baking powder and soda give these gluten free lemon poppy seed muffins their lovely rise, keep them tender, and neutralize the acidity of the lemon juice. Then, salt helps balance the flavors. (Paleo? See the FAQ below!)
  • POPPY SEEDS. Poppy seeds won’t really add much flavor-wise, but they’re a pretty addition to the muffins and give them their signature look. I get mine in the spices section of the grocery store.

Key Ingredient: Almond Flour

This recipe was specifically formulated with fine almond flour in mind. For best results and the perfect texture, look for finely ground, blanched almond flour (NOT almond meal, which has a coarser, grittier texture). Don’t try to substitute gluten-free 1:1 flour, coconut flour, or oat flour here. We usually find the best price on brands at Costco!


How To Make Almond Flour Lemon Poppy Seed Muffins, Step By Step

As always, you can find the full recipe with ingredient amounts, detailed instructions, and tips in the recipe card below.

making almond flour lemon poppy seed muffins step by step
  1. Preheat & Prep. To start, preheat oven temperature to 350 degrees F. Grease a muffin pan or line with parchment paper liners.
  2. Combine Wet Ingredients. In a large bowl, combine the wet ingredients. Stir together lemon zest, lemon juice, milk, syrup, oil, eggs, vanilla, and lemon extract (if using). Whisk until smooth.
  3. Add the dry ingredients. Next, add almond flour, tapioca starch, baking powder, baking soda, salt, and poppy seeds to the wet ingredients. Stir until just combined.
  4. Bonus Points: Let The Batter Rest. If you have time, I recommend letting the batter rest 30-60 minutes before baking. This gives the flour time to hydrate and the baking powder more time to work, which means you’ll get taller, more tender muffins!
  5. Bake Muffins. Scoop or spoon muffin batter into prepared muffin pan. (You can get 10 bigger muffins or 12 small muffins out of this batter.) If desired, sprinkle the tops of the muffins with turbinado sugar. Bake muffins at 350 degrees F. for 15-18 minutes, or until slightly golden brown and a toothpick inserted in the center comes out clean with just a few moist crumbs. Allow muffins to cool 1 minute in the muffin pan before transferring to a wire rack.
gluten-free almond flour lemon poppy seed muffins next to a bottle of milk

FAQ + Tips And Tricks For The Best Almond Flour Lemon Poppy Seed Muffins

PALEO? READ THIS. These can absolutely be made as paleo lemon poppy seed muffins, as almost every ingredient is paleo-approved. If you’re strictly paleo, you’ll want to substitute a paleo baking powder option and skip the optional dusting of turbinado sugar. All the other ingredients are A-ok!

CAN I USE ANOTHER FLOUR? Not in this recipe. I don’t recommend swapping in coconut flour or omitting the tapioca starch or arrowroot. This gluten-free lemon poppyseed muffins recipe was tested based on the moisture of the almond flour (which is different than white flour or gluten-free flour blends). The one exception is you *can* use cornstarch in place of the arrowroot or tapioca flour.

WHAT’S THE BEST WAY TO STORE LEFTOVER MUFFINS? I store leftover lemon poppy seed muffins in a bag or airtight container on the counter for 1-2 days, or in the refrigerator for 2-3. They’ll also keep up to a couple of months in the freezer!

THE BEST MUFFIN PANS & MUFFIN CUPS. For perfectly non-stick lemon poppy seed muffins, I recommend using parchment paper muffin liners like these in a metal muffin pan. You’ll get golden edges and the wrappers come right off. If you don’t want to fuss with liners, we love using a silicone muffin pan like this. They’re great and naturally nonstick!

gluten-free lemon poppy seed muffins cooling on a wire rack

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almond flour lemon poppy seed muffins stacked next to a bottle of milk

Almond Flour Lemon Poppy Seed Muffins (Gluten Free, Paleo)


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5 from 13 reviews

  • Author: Emily Dixon, One Lovely Life
  • Total Time: 25 minutes
  • Yield: 1012 Muffins 1x
  • Diet: Gluten Free

Description

These almond flour lemon poppy seed muffins have a light, fluffy texture and are BURSTING with bright lemon flavor. They’re the perfect yummy breakfast or snack!


Ingredients

Scale

Wet Ingredients:

  • 2 Tablespoons fresh lemon zest (from about 2 lemons)
  • 2 Tablespoons fresh lemon juice (about 1 lemon)
  • 1/3 cup milk* (I use unsweetened almond milk)
  • 1/3 cup pure maple syrup or honey
  • 1/4 cup avocado oil
  • 3 large eggs
  • 1 teaspoon vanilla extract
  • 1/2 teaspoon lemon extract or 1/4 teaspoon lemon oil

For the Dry Ingredients:

  • 2 1/2 cups blanched almond flour (finely ground)
  • 1/2 cup tapioca starch or arrowroot*
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 2 Tablespoons poppy seeds*

Optional: 2-3 tsp. turbinado sugar for decoration.


Instructions

  1. Preheat & Prep. To start, preheat oven temperature to 350 degrees F. Grease a muffin pan or line with parchment paper liners.
  2. Combine Wet Ingredients. In a large bowl, combine the wet ingredients. Stir together lemon zest, lemon juice, milk, syrup, oil, eggs, vanilla, and lemon extract (if using). Whisk until smooth.
  3. Add the dry ingredients. Next, add almond flour, tapioca starch, baking powder, baking soda, salt, and poppy seeds to the wet ingredients. Stir until just combined.
  4. Bake Muffins. Scoop or spoon muffin batter into prepared muffin pan. (You can get 10 bigger muffins or 12 small muffins out of this batter.) If desired, sprinkle the tops of the muffins with turbinado sugar. Bake muffins at 350 degrees F. for 15-18 minutes, or until slightly golden brown and a toothpick inserted in the center comes out clean with just a few moist crumbs. Allow muffins to cool 1 minute in the muffin pan before transferring to a wire rack.
  5. Store leftover muffins in an airtight container 1-2 days at room temperature. Or, freeze up to 2 months. 

Notes

  • Milk. You can use any kind of milk for this recipe–dairy or non-dairy. Whatever you drink!
  • Flour. No substitutes will work in this recipe for the almond flour. If you don’t have/can’t find tapioca starch or arrowroot, you can substitute cornstarch.
  • Poppy Seeds. Make sure to use poppy seeds or leave them out. I do NOT recommend trying to substitute chia seeds (which will absorb liquid from the muffin batter.)
  • Prep Time: 10 minutes
  • Cook Time: 15-18 minutes
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American

Nutrition

  • Serving Size: 1 Muffin
  • Calories: 230
  • Sugar: 7.1 g
  • Sodium: 126.1 mg
  • Fat: 18.1 g
  • Saturated Fat: 1.8 g
  • Carbohydrates: 13.3 g
  • Fiber: 2.9 g
  • Protein: 6.9 g
  • Cholesterol: 46.5 mg

Originally published March 2020. Fully updated with improved recipe notes, step by step photos and video and republished March 2025.

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38 Comments

  1. Lovely and easy. A keeper. Like your brownie recipe, I’ll be making this again and again. Thank you!

  2. Hi, I love your brownie recipe!! It’s the only one I make. I would like to make these muffins, but I would like to sub coconut sugar for the maple syrup. Is that possible? and if so how much would I use and would I have to increase the milk or oil by how much? and bake time? Thanks, for sharing. keep up the GREAT WORK!!!

    1. Hi, Theresa! I’m so glad you love the brownies! I don’t recommend coconut sugar in this recipe, since you’d have to make several other tweaks and it drastically changes the color of the muffins. In general, you need twice the amount of granulated sweetener as liquid, but I don’t feel like it’s a good 1:1 substitute for this recipe.

  3. I made this recipe and used potato starch to avoid going to the store and it turned out wonderfully. Thanks for the recipe. I’ll definitely make this for my gluten free friends.

  4. I’ve made this recipe a few times and it always turns out great. I do use chia seeds instead of poppy, which the author doesn’t recommend, but it always works for me. Also, I usually mix lemon juice and powdered sugar to make a glaze that takes them to the next level.

  5. I followed this recipe exactly and the muffins turned out so good! Even with having to substitute (with the suggested substitutions) since I didn’t want to make a trip to the store, I was very impressed that these turned out perfectly. It is so hard to find gluten free recipes that actually work and taste good! My kindergartner loves them and that is who I was hoping to please. Thank you so much!!!

    For the substitutions that are recommended/have a choice, I used:

    Coconut Milk instead of almond
    Canola Oil instead of avocado oil
    Lemon juice instead of lemon oil
    Cornstarch instead of arrowroot

  6. I made some changes because of my high cholesterol but this recipe allowed for these adjustments perfectly.
    Instead of 2.5 cups almond flour I did 1 cup and 1.5 cups oat flour. Used only 2 eggs. Added 1/2 cup of frozen wild blueberries. Thank you!

  7. I just found this found this recipe and it sounded great cholesterol wise but was very surprised at the 46.5mg amount. Could you let me know what ingredient is doing that? Thanks!

    1. Anne – That’ll be the eggs! I don’t recommend egg substitutes here since they’re crucial for the structure of the muffins. (Almond flour is a bit more finicky)