Lemon Almond Flour Muffins (High Protein)
If you think healthy baking has to mean dry, dense hockey pucks, these bright and zesty Lemon Almond Flour Muffins are about to change your mind. Made with a base of fine almond flour, protein powder, and fresh lemon juice, these muffins come together in a quick 15-minute prep and bake in under 18 minutes. They’re ultra-moist, naturally high in healthy fats, and packed with 8+ grams of protein per muffin.
As a dietitian, I love making baked goods that are healthy-ish like my Whole Wheat Blueberry Muffins or my Healthy Morning Glory Muffins.

Recipe Highlights
- Higher protein than traditional muffins thanks to the almond flour and protein powder
- Healthy ingredients you can feel good about eating
- Freeze for later to enjoy whenever a muffin craving strikes
Ingredient Notes

- Almond flour: Adds moisture, nutty flavor, and boosts protein and healthy fats while keeping the recipe gluten-free.
- Protein Powder: I love using collagen or an unflavored whey protein powder as they don’t have an aftertaste and keep the same texture to the muffins
- All-purpose flour: Provides structure and helps bind the ingredients for a soft, cohesive texture.
- Lemon juice and zest: Provides bright acidity, moisture, and amps up the lemony flavor.
- Maple syrup: Naturally sweetens the recipe plus adds moisture and flavor
Glaze (optional, but adds such yummy flavor!)
- ½ cup powdered sugar
- 1-2 tablespoons lemon juice
How to Make Lemon Almond Flour Muffins (Step by Step)


1. Preheat the oven to 350°F.
2, Line a muffin tin or grease your muffin tin well.
3. In a medium bowl, whisk together the eggs, lemon juice, lemon zest, maple syrup, oil, and vanilla extract.
4. In another medium bowl, mix together the almond flour, collagen, flour, baking soda, and salt.


5. Pour dry batter into the wet, mixing together, but don’t overmix.
6. Use a spoon or ice cream scoop to fill each muffin tin cup almost to the top.
7. Bake for 17-18 minutes—the top will start to brown and a toothpick will come out clean.
8. Once the muffins have cooled completely, make your glaze by whisking together the powdered sugar and the lemon juice until there are no clumps.
9. You can either add more sugar or more lemon juice, depending on how thick or how thin you want the glaze (I always prefer less liquid, so the glaze is super thick).
10. Drizzle the glaze on top of each muffin, and enjoy

Substitutions & Additions
- Blueberries: Fold in 1 cup of fresh or frozen blueberries for a delicious lemon-blueberry variation
- Poppy seeds: Mix in 1-2 tablespoons of poppy seeds for lemon poppy seed almond flour muffins
- Almond extract: Add ¼ teaspoon of almond extract to amp up the almond flavor

Tips from the Test Kitchen
- Overmixing can lead to dense muffins. Be careful to mix until just combined.
- An ice cream scoop can help you fill each muffin to a similar size.
- Overfilling can cause them to spill over the muffin tin during baking. Fill each muffin spot to just about 3/4 full.
Storage Suggestions
Store in an airtight container at room temperature for up to 3 days or in the refrigerator for up to a week.
These muffins freeze beautifully for up to 3 months. Wait to add lemon glaze until you’re ready to eat them.
More Healthy Baked Goods

Lemon Almond Flour Muffins (High Protein)
Ingredients
Dry Ingredients
- 2 ¼ cups almond flour
- ½ cup all-purpose flour
- ¼ cup protein powder collagen or unflavored whey
- 1 tsp baking soda
- ½ tsp salt
Wet Ingredients
- 3 eggs
- ½ cup lemon juice or about 3 lemons
- Zest of two lemons
- ½ cup maple syrup or honey
- ¼ cup avocado oil
- 1 ½ tsp vanilla extract
Lemon Glaze, optional
- 1/2 cup powdered sugar
- 1-2 tbsp lemon juice
Instructions
- Preheat the oven to 350°F, and line or grease a muffin tin.
- In a mixing bowl, mix dry ingredients: almond flour, protein powder, flour, baking soda, and salt.
- In another bowl, whisk together the wet ingredients: eggs, lemon juice, lemon zest, maple syrup, avocado oil, and vanilla.
- Combine wet and dry ingredients, mixing until just incorporated.
- Fill muffin cups about 3/4 full using an ice cream scoop.
- Bake for 17-18 minutes or until tops are golden and a toothpick comes out clean.
- Cool completely before glazing.
- For the glaze, whisk powdered sugar and lemon juice until smooth.
- Drizzle glaze over cooled muffins.
