keto lemon poppy seed muffins arranged on top of parchment paper with lemon curd

lemon poppy seed coconut flour muffins {keto, dairy-free}

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These lemon poppy seed coconut flour muffins are incredibly light, springy, and tender! Made entirely with coconut flour, this is a keto muffin recipe that is also gluten-free and dairy-free. Spread on some keto lemon curd or a low-carb strawberry rhubarb jam for an even more delicious low-carb breakfast or snack.

a hand holding a muffin with a bite taken out

Lemon and poppy seed will forever be a favorite combination. Each adds its own subtle flavor to these coconut flour muffins that results in a delicious (and healthy!) treat. Fresh lemon juice and lemon zest add the perfect citrus notes that pair beautifully with the nutty poppy seeds and a hint of cardamom (by the way, I love cardamom, especially with citrus).

benefits of coconut flour

I don’t often use only coconut flour in my keto baking, but it’s something I’m trying to do more as it’s really nutritious and filling, high in fiber, protein and MCTs. Also, it’s a great alternative to almond flour baked goods, especially if you’re nut-free or watching your almond flour intake. (For another low-carb coconut flour recipe, check out this keto coconut flour bread!)

how to use coconut flour

Unlike almond flour, coconut flour is not a 1:1 flour substitute. It’s really absorbent and dry, which means a little goes a long way (for instance, this entire recipe calls for just over 1/2 cup of coconut flour!). Because of its unique properties, coconut flour can be a bit tricky to work with, but this keto lemon poppy seed recipe is actually quite simple.

My best advice for working with coconut flour is to make sure you’re measuring correctly, since the smallest amount over or under can drastically change your results. Don’t pack it into the measuring cup– spooning it in and then leveling it off with the edge of a table knife is how I usually do it (for all flours, actually). The most accurate method? A kitchen scale is a really affordable investment and is especially helpful when working with keto-friendly ingredients like coconut flour.

keto lemon poppy seed muffins with lavender in the foreground

the ingredients

The biggest issue with coconut flour is that when it’s not used at the proper ratio, baked goods can turn out really dense and almost chalky. This coconut flour muffin recipe is essentially the opposite – four eggs give the muffins a fluffy texture (without tasting egg-y), while the freshly-squeezed lemon juice + leavening agents, and the baking method result in a nice, tall, and airy lemon poppy seed muffin.

  • eggs (at room temperature, pasture-raised when possible)
  • vanilla
  • almond extract (optional)
  • lemon zest
  • coconut oil (melted and cooled)
  • baking powder (preferably gluten-free and aluminum-free)
  • baking soda
  • granulated monk fruit sweetener
  • coconut flour
  • salt
  • cardamom (optional)
  • freshly-squeezed lemon juice
  • poppy seeds

let’s make keto coconut flour muffins!

The easy part! Did I mention these keto lemon poppy seed muffins only require one bowl? 🙂

First, prep a muffin tin with paper baking cups and preheat your oven to 425°F. It’s a much higher baking temperature than what we’d typically use, but we’ll turn it down later. The big blast of heat in the first few minutes of baking help these coconut flour muffins rise and get a little taller than they would if they went in at 350°F.

  1. In a large mixing bowl, whisk together the eggs, vanilla, almond extract, lemon zest, and coconut oil. Make sure the eggs are at room temperature- you can do this quickly by letting them sit in a bowl of warm water. Coconut oil will solidify when mixed with cold eggs, which is why room temp eggs are best. Tip: wait to add the lemon juice (I explain this below)!
  2. Mix in the dry ingredients: monk fruit sweetener, coconut flour, baking powder, baking soda, salt, cardamom, and poppy seeds. Stir in the lemon juice last since the acid will react with the baking powder and baking soda- you want that to occur right before baking.
  3. Spoon into muffin tin and bake. Fill each baking cup with about 1/4 cup of the muffin batter (I usually get 7 muffins). Place the muffin tin in the oven and bake at 425°F for 5 minutes, then turn the temperature down to 350°F and bake for 11-13 minutes. Remove, cool, and enjoy!

for the best keto lemon poppy seed muffins

  • Use parchment paper baking cups! I’ve found they easily peel away from the muffin, while some types of baking cups stick and the muffin breaks away with it.
  • Don’t forget to set the timer for those first 5 minutes of baking at a higher temperature! Turn it down to 350°F immediately after 5 minutes.
  • The muffins are done when the edges are slightly browned and a toothpick inserted in the center comes out clean.
  • Room temperature ingredients work best and will prevent the melted coconut oil from solidifying and making the batter lumpy.
  • Store muffins covered, at room temperature for up to five days, and in the freezer for up to two months.

I hope you enjoy these keto lemon poppy seed coconut flour muffins! This easy, one-bowl recipe makes the perfect, low-carb and high protein meal to start off your day. Plus, it’s also dairy-free and gluten-free and is in the oven baking in less than 10 minutes. Easy enough to make on a weekday morning! Can’t beat that.

need more keto muffin recipes in your life?

In case you do…

If you give these a try, let me know! Drop a comment below, leave a five-star review, or tag @stemandspoon on Instagram! I love to see what you create.

you might also love…

*This post contains Amazon affiliate links. I earn a small commission (at no extra cost to you) when you purchase something from one of those links. I will always recommend brands and products that I use and love. Thank you for supporting Stem and Spoon! -Abby

horizontal image of a bite taken out of a coconut flour muffin

lemon poppy seed coconut flour muffins {keto, dairy-free}

Yield: 7 muffins
Prep Time: 10 minutes
Cook Time: 16 minutes
Additional Time: 5 minutes
Total Time: 31 minutes

Tender and fluffy with a subtle citrus flavor, these keto lemon poppy seed muffins make a delicious breakfast or snack! They're an easy coconut flour muffin recipe that is also gluten-free, dairy-free, and nut-free.


  • 4 eggs, at room temperature (pasture-raised when possible)
  • 1 teaspoon vanilla extract
  • 1/4 teaspoon almond extract (optional)
  • 1 tablespoon lemon zest
  • 1/4 cup coconut oil, melted and cooled
  • 1/2 cup + 2 tablespoons coconut flour (preferably sifted)
  • 1/4 cup granulated monk fruit sweetener
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1/4 teaspoon cardamom (optional)
  • 2 tablespoons poppy seeds
  • 1/4 cup fresh lemon juice


  1. Preheat the oven to 425°F. Line a standard sized muffin tin with parchment paper baking cups (you'll only need 7-8).
  2. In a large mixing bowl, whisk together the eggs, vanilla, almond extract, lemon zest, and coconut oil. Mix until well-combined.
  3. Add in the coconut flour, monk fruit sweetener, baking powder, baking soda, salt and cardamom. Stir to combine, then mix in the poppy seeds.
  4. Next, mix in the lemon juice (this is reserved for last since the acid reacts with the baking powder/soda and is best when immediately transferred to a hot oven).
  5. Spoon about 1/4 cup batter into each of the baking cups (they'll be about 3/4 full).
  6. Transfer to the oven and bake at 425°F for 5 minutes. The initial blast of heat reacts with the baking powder and results in a taller muffin.
  7. After 5 minutes, turn the temperature down to 350°F. Bake another 11-13 minutes. The edges should be a light golden brown and a toothpick inserted in the center of a muffin should come out clean.
  8. Remove the muffin pan from the oven and let them cool for about 5 minutes in the pan. Transfer them to a baking rack to cool completely.
  9. Serve plain, with keto lemon curd, or a low-carb jam!


Room temperature eggs will work best. If cold, the eggs could lead to the melted coconut oil solidifying and turning the batter lumpy. To quickly take the chill off the eggs, place them in a bowl of warm water for 5-10 minutes.

Store the lemon poppy seed muffins covered, at room temperature for up to five days, and in the freezer for up to two months.

Nutrition Information:
Yield: 7 Serving Size: 1
Amount Per Serving: Calories: 143Total Fat: 12gSaturated Fat: 8gTrans Fat: 0gUnsaturated Fat: 3gCholesterol: 106mgSodium: 278mgCarbohydrates: 4gNet Carbohydrates: 3gFiber: 1gSugar: 2gProtein: 5g

This nutritional information is approximate and is provided for convenience as a courtesy.

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