These healthy Lemon Chia Seed Muffins have a base of almond flour, coconut sugar, and Greek yogurt. Fresh lemon juice and zest makes the muffins bright and tart. And chia seeds are a great substitute for poppyseeds while providing fiber, healthy fats, and protein.

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The Best Gluten-Free Muffins
These Lemon Chia Seed Muffins are the best way to start the day. They're packed with good-for-you ingredients and are incredibly moist, soft, and delicious. The muffins are filled with citrus goodness while the chia seeds give a light crunch. And the sticky glaze on top is sweet and sour, leaving you wanting more and more!
These are great for breakfast or dessert and are perfect to take on-the-go as a snack. They only take 45 minutes from start to finish and couldn't be easier to whip up!
Is This Healthy?
Absolutely! We use almond flour and arrowroot starch as a base, and use thick Greek yogurt to provide lots of moisture and healthy fats. If you are avoiding refined sugars, you can simply omit the lemon glaze.
Chia seeds have become a popular health food for many reasons. They're low in calories and are a great source of fiber, protein, healthy omega-3 fat, and antioxidants. They pack quite a punch and have become one of my pantry staples.
Ingredients
- Greek yogurt: Adds plenty of moisture, richness, and protein. I always recommend using full-fat yogurt - it tastes better and is more satiating. Also, skim or low-fat products tend to be loaded with sugar to make up for the lack of fat (and therefore, flavor).
- Lemon juice and zest: Fresh is key to providing that burst of citrus flavor.
- Egg: To bind all the ingredients together. Use room temperature for best results.
- Almond flour: The gluten-free base of our muffins.
- Arrowroot starch: Helps to add structure and density to gluten-free and grain-free baked goods.
- Coconut sugar: My favorite sweetener because it's unrefined and plant-based. You can substitute with an equal amount of white granulated sugar.
- Chia seeds: Provides crunch and nutrition in place of poppy seeds.
- Baking soda and baking powder: Both give rise to the muffins to make them soft and fluffy.
- Salt: To enhance the flavor.
For The Lemon Glaze
- Powdered sugar and milk: Classic icing ingredients.
- Lemon juice: Add a little to make a deliciously sweet and sour glaze.
How To Make It
- Preheat the oven. Start by preheating the oven to 350°F and lining a muffin tin with cupcake liners.
- Combine the dry ingredients. Mix together the almond flour, arrowroot starch, chia seeds, baking soda, baking powder, and salt until evenly combined. Set aside.
- Whisk together the wet ingredients. In a large bowl, whisk together the egg and coconut sugar until homogenous. Then add the yogurt, lemon juice, zest, and extract (if using) and whisk together. Stir in the dry ingredients.
- Bake and make the glaze. Scoop a scant ¼ of the batter into the muffin tins. Bake for 15-20 minutes or until a toothpick comes out clean. Meanwhile, make the glaze by whisking together the confectioner's sugar, lemon juice, and milk.
- Serve. Let the muffins cool completely on the countertop. Then spoon a little glaze over the tops and serve.
Top Tips
- Use fresh lemon juice. Fresh is best for maximum lemon flavor, plus you get a lot of flavor and oils from the zest itself. Leave the lemon out on the countertop to let it get to room temperature - warm citrus have more juice.
- For best results, use a thick yogurt. My favorites are Greek or European style. And always use full-fat! The skim versions are loaded with sugar and preservatives to make up for the lack of richness.
- Avoid overfilling the muffin liners. I like to use a scant ¼ cup or cookie scooper to fill the tins barely ¾ full.
Substitutions and Variations
- Substitute the coconut sugar with an equal amount of white cane sugar.
- Substitute arrowroot starch with an equal amount of tapioca flour.
- Add a scoop of collagen peptides for a boost of protein.
- Add ½ teaspoon almond or vanilla extract for a fun flavor combo.
Storing & Freezing
Storing: Store leftover Lemon Chia Seed Muffins in a zip-top bag or airtight container. They'll last 3-4 days at room temperature or 5-6 days in the fridge. You can choose to store the muffins glazed or with the glaze in a separate container.
Freezing: Let cool completely. Place in a freezer-safe, air tight container or zip-top bag with as much air removed as possible. Store in the freezer for up to 3 months. Let thaw in the fridge or on the counter overnight.
FAQ
Chia seeds and poppy seeds are both small, black seeds. The main difference is that chia seeds soak up a lot of liquid to become a gel-like consistency. So the texture of chia seeds will change when introduced to a liquid but poppy seeds do not.
Poppy seeds are a great source of manganese, fiber, and calcium. Chia seeds are full of fiber, protein, omega-3 fatty acids, and antioxidants. Both have nutritional benefits and can fit into a healthy diet.
I love adding chia seeds to baked goods, smoothies, cereals, and granolas. They also are great with some milk or liquid to create a chia seed pudding.
Looking For More?
You can never have too many healthy and delicious snacks on hand! For more satisfying snack ideas, try these:
- Pumpkin Protein Balls
- Lemon Dill Hummus
- Healthy Apple Chai Bars
- Healthy Almond Cupcakes
- Banana Chocolate Chip Walnut Muffins
📋 Recipe
Lemon Chia Seed Muffins
Equipment
- Muffin tin
Ingredients
- 2 cups almond flour
- ¼ cup arrowroot starch
- 2½ tablespoon chia seeds
- ½ teaspoon baking soda
- 1 teaspoon baking powder
- ¼ teaspoon salt
- 1 egg
- ½ cup coconut sugar
- ½ cup full-fat Greek yogurt
- 3 tablespoon lemon juice about 1 small lemon
- Zest from one lemon
- 1 teaspoon lemon extract (optional)
Glaze
- ⅓ cup confectioner's sugar sifted
- ½ tbsp lemon juice
- 1 tablespoon milk
Instructions
- Preheat to 350F. Line a muffin tin with liners.
- In a bowl, combine almond flour, arrowroot starch, chia seeds, baking soda, baking powder, and salt. Whisk to evenly combine. Set aside.
- To a large bowl or stand mixer, whisk egg and coconut sugar until homogenous. Add yogurt, lemon juice, zest, and lemon extract, if using. Stir until combined.
- Add the dry ingredients to the wet and stir well.
- Scoop a scant ¼ cup of the batter into each liner. Bake for 15-20 minutes or until inserted toothpick comes out clean. Let cool completely.
Lemon Glaze
- Whisk sifted confectioner's sugar, lemon juice, and milk together until smooth.
- Spoon glaze over the tops of the cooled muffins.
Notes
- Storing: Store muffins in a zip-top bag or airtight container. They'll last 3-4 days at room temperature or 5-6 days in the fridge. You can choose to store the muffins glazed or with the glaze in a separate container.
- Freezing: Let cool completely. Place in a freezer-safe, air tight container or zip-top bag with as much air removed as possible. Store in the freezer for up to 3 months. Let thaw in the fridge or on the counter overnight.
- Substitutions/Variations:
- Substitute the coconut sugar with an equal amount of white cane sugar.
- Substitute arrowroot starch with an equal amount of tapioca flour.
- Add a scoop of collagen peptides for a boost of protein.
- Add ½ teaspoon almond or vanilla extract for a fun flavor combo.
Nutrition
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Products I Used
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