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Lemon Poppy Seed Muffins

These Lemon Poppy Seed Muffins are moist, sweet and brimming with zesty lemon flavor. Enjoy the delicious taste of homemade muffins without the midmorning sugar crash!

We love starting our mornings with a hot cup of coffee and a little something sweet. If you like today’s muffin recipe, these Chocolate Chip Muffins are another keto-approved breakfast pastry to try next!

Lemon poppy seed muffins stacked on a white plate.

Why These Muffins are Best

A perfect balance of sweetness and tart lemon makes these muffins completely irresistible. Our lemon poppy seed muffins taste just like the ones you love from the bakery while keeping your on track with your wellness journey.

  • Packed with fresh lemon flavor.
  • All natural ingredients.
  • Super moist and perfectly sweet.
  • Flecked with poppy seeds.
  • Freezer friendly.
  • Gluten free with no added sugars!

Ingredient Notes

Ingredients needed to make lemon poppy seed muffins.
  • Eggs. We use three large eggs to bind these lemon muffins. Because gluten free flours don’t contain as much protein as wheat flour, the added protein from the eggs is essential if you want your muffins to hold shape.
  • Lemons. You will need both the zest and the juice of two full lemons to give these muffins their citrusy aroma and taste.
  • Granulated monk fruit. This is our favorite sugar-free sweetener for baking because it’s all natural with a mild flavor.
  • Almond flour. Compared to most grain-free flours, almond flour is high in protein and has a neutral flavor making it perfect for all kinds of baked goods.
  • Poppy seeds. They add a slight nutty flavor to the muffins while giving them an appealing appearance.

Tips and Tricks

Lemon muffin batter unbaked in a cupcake tin.
  • Grease your muffin tin! Use shortening to coat the wells of your muffin pan before adding the batter to prevent sticking. Or line the muffin pan with paper cupcake liners instead.
  • Zest the lemons before juicing. Removing the zest softens the lemons so they release more juice when squeezed.
  • Do not overbake. These Lemon Poppy Seed Muffins will dry out quickly if left in the oven too long. Take them out of the oven as soon as toothpick inserted into the center of one muffin comes out clean.
Lemon muffins on green plate.

Recipe FAQs

Can I use a different sugar substitute for muffins?

Yes, other granulated sugar substitutes for baking will work. If you don’t have monk fruit (or prefer not to use it), we found granulated erythritol tasted great in these muffins as well.

How should lemon muffins be stored?

Store these keto Lemon Poppy Seed Muffins in an airtight container at room temperature for up to 3 days. Or you can freeze them for up to 3 months!

What’s the best way to zest a lemon?

Use a handheld zester or grating tool. Hold the lemon in one hand over a bowl. Hold the zesting tool in your other hand and run the blades (or grating holes) along the peel of the lemon rind. Be careful to remove only the outermost yellow layer of the peel (zest).

Are these muffins paleo?

Yes, these grain free muffins can be part of a paleo diet. They are also keto, low carb, gluten free and dairy free!

Can I double the recipe to make more?

You can absolutely double it! You will get about 18 regular sized muffins from this recipe if you double the ingredients.

More Easy Breakfast Recipes

These Lemon Poppy Seed Muffins are moist, sweet and brimming with zesty lemon flavor. Enjoy the delicious taste of homemade muffins without the midmorning sugar crash!

Lemon Poppy Seed Muffins

Yield: 9 muffins
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

These Lemon Poppy Seed Muffins are moist, sweet and brimming with zesty lemon flavor. Enjoy the delicious taste of homemade muffins without the midmorning sugar crash!


  • 3 large eggs
  • 1 teaspoon vanilla extract
  • 1/2 cup vegetable oil
  • 2 lemons, zested and juiced
  • 1/2 cup granulated monk fruit
  • 2 teaspoons baking powder
  • 1/2 teaspoon kosher salt
  • 2 3/4 cup almond flour
  • 1 Tablespoon poppy seeds


  1. Preheat oven to 350 degrees F. Line a muffin pan with paper liners or use shortening to grease muffin cavities.
  2. Beat the eggs in a large bowl. Add vanilla extract, vegetable oil, lemon zest (about 2 teaspoons). Whisk everything together, then add monk fruit, baking powder, salt, and 1/4 cup lemon juice. Stir well to combine.
  3. Add almond flour and combine completely. Fold in poppy seeds.
  4. Divide the batter into nine muffin tins.
  5. Bake for 25 minutes or until a toothpick comes out clean. Be careful not to overbake, as it drys them out.
  6. Let muffins cool before serving.


  • Store in airtight container at room temperature for up to 3 days or freeze for up to 3 months.
  • Swap out monk fruit for granulated erythritol if desired.
Nutrition Information:
Yield: 9 Serving Size: 1 muffin
Amount Per Serving: Calories: 347Total Fat: 31gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 27gCholesterol: 62mgSodium: 203mgCarbohydrates: 11gFiber: 5gSugar: 3gProtein: 10g

The best gluten free, sugar free Lemon Poppy Seed Muffins are easy to make with the perfect soft crumb. Enjoy them now or freeze for later!


Tuesday 14th of May 2024

Hello, how critical is vegetable oil to this recipe? could I sub with a sat fat like coconut oil- or could I use avocado oil?


Thursday 21st of September 2023

Would blueberries work in this recipe?


Sunday 5th of June 2022

Can sub the almond flour with all-purpose flour?


Monday 6th of June 2022

These are made specifically for almond flour and were not tested with all-purpose flour. Sorry.

Mary Ann

Sunday 5th of June 2022

I was wondering if you have ever tried Swerve Products in you baking? If you ever do, I would be interested in your results, and how they work as opposed to other low calorie natural sweeteners.


Monday 6th of June 2022

The swerve products work great in all my recipes. I personally just prefer monkfruit sweetener, as it doesn't leave as much of a cooling effect on your mouth.

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