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Home » Recipes » Desserts

Almond Flour Lemon Poppy Seed Cupcakes

Last Updated: May 18, 2026 by Leanne Combden

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Gluten-free and bursting with fresh citrus and poppy seeds, these almond flour lemon poppy seed cupcakes have a tart lemon curd filling and a velvety, stable whipped cream cheese frosting. They're a light and lemony dessert, and a fun twist on my gluten-free lemon poppy seed cake!

Cupcake on a parchment wrapper with some removed to show the lemon curd inside.

Quick Look: Lemon Poppy Seed Cupcakes

  • ⏱ Prep Time: 25 minutes
  • 👩🏻‍🍳 Bake Time: 15 minutes
  • 🆒 Cooling Time: 1 hour
  • ⏳ Total Time: 1 hour 40 minutes
  • 🧁 Servings: 12 cupcakes
  • ⚡ Calories: 392 per cupcake
  • 🍽 Diet: gluten-free
  • 🔥 Flavor/texture: soft and tender with a slight tart lemon flavor and a smooth and creamy whipped topping.
  • 👌 Difficulty: surprisingly easy, just requires a bit of time to fill and pipe.
  • ❤️ Why you'll love: perfect rise, uses store-bought lemon curd, stabilized whipped cream lasts for days.

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The secret behind these incredible cupcakes

Want to know how these cupcakes get their amazing flavor and texture while staying completely gluten-free (and easy)? It comes down to a few simple tricks:

  1. Almond flour + cornstarch: This gluten-free blend creates a light, tender crumb. The cornstarch absorbs excess oil from the almond flour, keeping the cupcakes perfectly moist instead of dense. (It's this combo that ensures my gluten-free marble cake has such a tender and fluffy crumb).
  2. Whipped eggs & sugar: Beating the eggs and sugar with an electric mixer until bubbly helps dissolve the sugar and incorporate air. This step ensures the gluten-free batter rises beautifully. (I use this process for a number of recipes, including my almond flour vanilla cupcakes).
  3. Store-bought lemon curd: We're swapping homemade curd for a high quality jarred version to save time without sacrificing that bright, tart lemon flavor.
  4. Stabilized whipped cream frosting. I usually serve my almond flour lemon cake with whipped cream, so I wanted that combo for these cupcakes too. But, traditional whipped cream wilts quickly on cupcakes. By blending it with cream cheese, you get a light, airy frosting that holds its shape, pipes perfectly and adds a delicious, subtle tang.
Table of Contents
  • Quick Look: Lemon Poppy Seed Cupcakes
  • The secret behind these incredible cupcakes
  • Ingredient notes
  • How to make lemon poppy seed cupcakes with almond flour
  • Expert tips for making these cupcakes
  • Measuring your ingredients
  • Lemon poppy seed cupcakes FAQ
  • Other recommended cupcake recipes
  • 📖 Recipe

Ingredient notes

Ingredients to make lemon poppy seed cupcakes and frosting arranged individually and labeled.
  • Almond flour - Using almond flour results in a softer crumb for cakes and cupcakes compared to almond meal. (You can see from my other almond flour recipes that it's what I use most of the time). Both come from raw ground almonds, but almond flour consists of blanched almonds with the skins removed to ensure a finer consistency.
  • Lemons - Grab about 2 medium lemons for this recipe. You will need 2 tablespoons of zest for the cupcakes and some of the lemon juice for both the batter and frosting.
  • Poppy seeds - Just 1 tablespoon is all you need.
  • Eggs - You'll need 4 large eggs to help these gluten-free cupcakes rise. Don't forget to let them come to room temperature first.
  • Sugar - I'm using granulated sugar but you can easily substitute with cane sugar.
  • Almond extract - Just a little really gives these cupcakes a bakery worthy flavor (just like it does with my gluten-free lemon blueberry bread).
  • Oil - I used olive oil but extra virgin olive oil, avocado oil or vegetable oil will work too.
  • Heavy whipping cream - Use cold, heavy whipping cream that's at least 35% milk fat.
  • Cream cheese - The recipe calls for just 6 tablespoons of full fat cream cheese. Keep it cold. You don't need to let it come to room temperature for the frosting like you would for my peanut butter cream cheese frosting.
  • Powdered sugar - This will work with the cream cheese to stabilize the whipped cream but also to sweeten it.

How to make lemon poppy seed cupcakes with almond flour

Almond flour and other dry ingredients whisked together in a glass bowl.

Step 1: Whisk together the almond flour, cornstarch, poppy seeds, baking powder and salt.

Eggs and sugar whipped together in a large bowl until bubbles formed on top.

Step 2: In a large bowl, use an electric mixer on medium-high speed to beat together the eggs and sugar until bubbly on top, about 1 minute.

All the wet ingredients mixed together in a glass bowl.

Step 3: Add in the oil, lemon juice, zest and almond extract. Mix until just combined.

Cupcake batter fully mixed together in a bowl with a spatula.

Step 4: Add the dry ingredients to the wet mixture, switch to a spatula, and stir until just combined.

Cupcake batter divided into cupcake pan lined with parchment liners.

Step 5: Divide the batter into a 12 cup muffin pan (with liners), filling them about ¾ full.

Cupcakes baked in the cupcake pan.

Step 6: Bake at 350F for 13-15 minutes. Let cool for 5 minutes in the pan, then transfer to a wire rack to cool completely.

Cupcakes on a wire rack with center holes carved out and lemon curd in a piping bag.

Step 7: Cut a circle into the top of each cupcake, about 1-inch deep. (You can use a knife, but I normally use the bottom of a piping tip as seen in the photo).

Lemon curd piped into cupcakes.

Step 8: Spoon or pipe the lemon curd into each of the carved out circles. (You'll use about half of the curd for this step).

Cream cheese whipped cream mixed together in a bowl with beaters.

Step 9: Make the frosting by first whipping together the cream cheese and lemon juice. Then, beat in the powdered sugar. Next, gradually add in the whipping cream. Increase speed to medium-high and beat until stiff peaks form.

Whipped cream piped onto cupcakes with more lemon curd piped on top.

Step 10: Pipe the frosting onto the cupcakes, leaving a center in the middle and then spoon or pipe the remainder of the lemon curd into each cupcake.

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Expert tips for making these cupcakes

  • Be careful not to over whip the sugar and eggs. You just need to beat them together for about a minute in order to get the mixture foamy with bubbles on top. If you whip them for too long, the mixture will increase in size. This will add too much liquid to the batter and make it too runny.
  • Let the cupcakes completely cool. In order to carve out centers for the lemon curd, you need the cupcakes to be fully cooled. This is also important for the whipped cream topping. It will just melt off if the cupcakes are still warm.
  • Making the frosting. Gradually add the heavy cream to the cream cheese mixture so it has time to mix in evenly. Once fully blended, you can increase the mixer speed. Be careful not to overmix. Once you hit stiff peaks, stop the mixer. The frosting can start to quickly curdle if you whip it for too long.

Measuring your ingredients

For convenience, US cup measurements are included in the recipe card for this recipe. To ensure greater accuracy, however, weight and volume measurements are also provided. So, if you see grams (g), you'll want to use a kitchen scale to weigh your ingredients, and if you see milliliters (ml), you'll want to use a liquid measuring cup. Smaller quantities of ingredients are provided in teaspoons and tablespoons.

A bunch of cupcakes arranged on a pink surface.

Lemon poppy seed cupcakes FAQ

Why did my cupcakes sink in the middle?

There are three main reasons this could happen:
The cupcake pan was too full. You only want to fill each cupcake cavity ¾ full. If the cupcakes don't have room to expand as they bake, they may deflate when you take them out of the oven. A sunken appearance could also be from the batter being over mixed. This will aerate the batter too much and create a sunken, dense cupcake. Lastly, the cupcakes might not have been baked for long enough.

Can I leave out the curd and use a different frosting for these cupcakes?

Yes, you can leave the curd out if you prefer. As for frosting options, if you prefer a buttercream style, this vanilla sour cream frosting is a little sweeter and great for piping. If you love the combination of lemon and chocolate, this sour cream chocolate frosting is smooth and rich like ganache and perfectly pipe-able!

What's the best way to store these lemon cupcakes?

Since they're filled with lemon curd and topped with cream cheese whipped cream, they should be stored in a sealed container in the fridge. In my experience, they stay moist and tender and the whipped cream frosting stays stable for 5-6 days.

Can I make these cupcakes with another type of citrus?

Absolutely! You can substitute orange or lime in this cupcake recipe. I know the flavors work well as my almond orange cake recipe and gluten-free coconut lime cake are both made with almond flour and ridiculously delicious!

Other recommended cupcake recipes

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📖 Recipe

A lemon poppy seed cupcake with some removed to show the lemon curd filling inside.

Almond Flour Lemon Poppy Seed Cupcakes

These Almond Flour Lemon Poppy Seed Cupcakes are gluten-free with a tart lemon curd filling and a creamy, stable whipped cream cheese frosting.
5 from 1 vote
Print Pin
Prep Time: 25 minutes minutes
Cook Time: 15 minutes minutes
Cooling Time: 1 hour hour
Total Time: 1 hour hour 40 minutes minutes
Servings: 12 cupcakes
Author: Leanne Combden

Ingredients

For the cupcakes:

  • 2 ¼ cups (234 g) fine blanched almond flour
  • 2 tablespoons (15 g) cornstarch
  • 1 tablespoon poppy seeds
  • 1 teaspoon baking powder
  • ½ teaspoon fine sea salt
  • 4 large eggs, room temperature
  • ½ cup (110 g) granulated sugar
  • ¼ cup (60 ml) olive oil
  • 2 tablespoons lemon zest, about 2 medium lemons
  • 1 tablespoon freshly squeezed lemon juice
  • ¼ teaspoon almond extract
  • 1 cup (230 g) lemon curd, bought or homemade

For the frosting:

  • 6 tablespoons (85 g) full fat cream cheese, cold and cubed
  • ½ teaspoon freshly squeezed lemon juice
  • 1 cup (120 g) powdered sugar, sifted if lumpy
  • ¾ cup (180 ml) heavy whipping cream

Instructions

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Make the cupcakes:

  • Preheat oven to 350F and line a cupcake pan with 12 parchment liners.
  • In a medium-sized bowl, whisk together the almond flour, cornstarch, poppy seeds, baking powder and salt.
  • In a large bowl, use an electric mixer on medium-high speed to beat together the eggs and sugar until bubbles form on top, about 1 minute.
  • Add in the oil, lemon zest, lemon juice and almond extract. Mix until just combined.
  • Add the dry ingredients to the wet mixture, switch to a spatula, and stir until just combined.
  • Divide the batter into the 12 cupcake liners, filling each one about ¾ full.
  • Bake for 13-15 minutes, or until a toothpick inserted into a cupcake comes out clean. Let cool for 5 minutes in the pan, then transfer to a wire rack to cool completely.
  • Cut a circle into the top of each cupcake, about 1-inch deep. (You can use a knife, but I normally use the bottom of a piping tip to carve it out).
  • Spoon or pipe some of the lemon curd into each of the carved out circles. (You'll use about half of the curd).

Make the frosting:

  • First, whip together the cold cream cheese and lemon juice and then beat in the powdered sugar. The mixture should resemble runny cream cheese frosting.
  • On low speed, gradually add in the cold whipping cream until it's mixed into the cream cheese mixture. Once everything is combined, increase the speed to medium-high and beat until stiff peaks form.
  • Pipe the frosting onto the cupcakes, leaving a center in the middle and then spoon or pipe in the remainder of the lemon curd.

Notes

  1. Be careful not to over whip the sugar and eggs. You just need to beat them together for about a minute in order to get the mixture foamy with bubbles on top. If you whip them for too long, the mixture will increase in size. This will add too much liquid to the batter and make it too runny.
  2. Let the cupcakes completely cool. In order to carve out centers for the lemon curd, you need the cupcakes to be fully cooled. This is also important for the whipped cream topping. It will just melt off if the cupcakes are still warm.
  3. Making the frosting. Be careful not to overmix. Once you hit stiff peaks, stop the mixer. The frosting can quickly curdle if you whip it for too long.

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Nutrition Facts per Serving

Calories: 392kcal | Carbohydrates: 38g | Protein: 9g | Fat: 24g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.05g | Cholesterol: 80mg | Sodium: 284mg | Potassium: 72mg | Fiber: 3g | Sugar: 32g | Vitamin A: 317IU | Vitamin C: 2mg | Calcium: 129mg | Iron: 1mg

Disclaimer

Nutrition information is an estimate only and will vary depending on the substitutions made and the brands used.

Did you make this recipe or have any questions?

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  1. Leanne Combden says

    May 18, 2026 at 2:02 pm

    5 stars
    I'm so excited to finally share this recipe! While I had the recipe nailed down after the second time making it, I ended up making it a few more times to test it with different frostings, without lemon curd and without poppy seeds. I'm so happy with the final recipe, and it's been approved by a number of taste testers too!

    Reply
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Hey there! I'm Leanne and welcome to Crumb Top Baking. I'm a self-taught baker, home cook and food photographer, and I'm passionate about sharing well-tested, simple and approachable desserts and savory recipes

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