Lemon Chia Seed Muffins
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Fluffy and full of citrus flavor, Lemon Chia Seed Muffins are a tasty breakfast treat or healthy snack. Naturally sweetened with honey and made with oat flour, our lemon muffin recipe is gluten free!
If you’re looking for a healthy and delicious make-ahead breakfast, Lemon Chia Seed Muffins are for you! In addition to being full of omega-3 fatty acids, they are also low in sugar.
Plus, they’re super easy to make in one bowl.
Tips for the best Lemon Chia Seed Muffins
- When measuring the oat flour, be sure to use the “spoon and level” method to prevent overpacking.
- Add the oat flour to the wet ingredients and mix well to allow the oat flour to absorb some of the moisture and get fully incorporated into the batter.
- Chilling the batter before scooping it into the muffin tin helps to achieve a better rise and results in a more tender muffin. Chilling allows the baking powder to start activating before it is heated. I recommend chilling for 30 to 60 minutes, but you can absolutely chill longer. Chilling overnight produces the highest domes, but the batter shrinks and stiffens quite a bit because the chia seeds absorb a lot of moisture. Because we chill the batter, this recipe works a little better with liquid oil instead of coconut oil. If you are in a hurry, you can skip chilling, but the muffins will come out a little flatter.
- Avoid overfilling the muffin wells. These muffins (especially if you skip chilling) will spill over the sides if overfilled. Aim for about ¾ of the way full.
Ingredients
Substitutions
Greek Yogurt – We used full-fat plain Greek yogurt in this recipe, but I also tested fat-free plain Greek yogurt, and both worked well, so use whatever you have on hand. Regular yogurt or buttermilk would probably work but we haven’t tested it, so try at your own risk! The yogurt adds protein and moisture to these muffins so it’s an important ingredient!
Honey – Maple syrup or even granulated sugar can be used instead of honey in this recipe. When using granulated sugar, the muffins took a few extra minutes to bake and were lighter in color. Honey in combination with oat flour creates a dark golden color after baked, so keep this in mind when assessing if the muffins are fully cooked.
Eggs – I did not test any egg replacements in this recipe. If you try one, we would love to know how it worked in the comments below!
Avocado Oil – Any neutral flavored cooking oil can be used in this recipe. Melted coconut oil works but produced slightly less tender muffins. If using melted coconut oil, allow the coconut oil to cool slightly and allow the Greek yogurt and eggs to come to room temperature before combining to prevent the coconut oil from solidifying and not mixing in well. I haven’t tried these with melted butter, but I think it might work!
Lemon Juice & Zest – Fresh lemon juice and lots of lemon zest make this recipe packed full of lemon flavor – don’t skip it!
Lemon Extract – Lemon extract adds a little additional lemon flavor to these muffins without adding too much acid to the recipe. You can skip it if you don’t have it but I would add a little bit more lemon zest!
Almond Extract – Almond extract is optional but is so delicious in these muffins. It gives poppyseed muffins their trademark flavor and pairs really well with lemon. You can substitute vanilla extract if you do not have almond extract on hand or if you do not like it.
Oat Flour: Either store-bought or homemade oat flour will work. If using homemade oat flour, ensure the oats are processed into a very fine powder, with no oats visible. Check out this post on making homemade oat flour for a full tutorial. If you need this recipe to be gluten-free, be sure to select gluten-free oat flour or gluten-free old-fashioned oats to make oat flour with. You can not use almond flour or coconut flour in place of oat flour.
Baking Powder & Baking Soda – Both are used in these lemon chia muffins because the Greek yogurt and lemon juice are both acidic and require a little additional leavening to achieve a rise. This recipe works the best when the batter is chilled before baking, as it allows the baking powder to activate beforehand.
Black Chia Seeds: The chia seeds put a healthier spin on classic lemon muffins. White chia seeds work, but aren’t as pretty. Poppy seeds work as a 1:1 substitute for chia seeds.
Gluten Free: If you want to make these muffins gluten free, make sure to use gluten-free oat flour. While oats do not contain gluten, many facilities process them on shared equipment with gluten-containing grains. This can be a source of cross contamination.
Vegan: We haven’t tried making these muffins vegan. You could try dairy free yogurt and an egg substitute, but I’m not sure how it would work.
Muffin Liners: Silicone muffin liners work well. They do take just a minute or two longer to bake in silicone liners. When using paper liners, be sure to allow the muffins to cool for at least 5-10 minutes before removing them from the liners so that they remove cleanly.
Helpful Tools
It is also helpful to have a nonstick muffin tin or silicone muffin liners. This citrus zester and citrus juicer are also helpful!
We love this muffin pan because it is nonstick!
Do I have to chill the batter?
Chilling the batter before scooping it into the muffin tin helps to achieve a better rise and results in a more tender muffin.
Chilling allows the baking powder to start activating before it is heated. I recommend chilling for 30-60 minutes, but you can absolutely chill longer. I did
Because we chill the batter,
How to Make Lemon Chia Muffins
- Whisk wet ingredients together until smooth. Next, stir in the dry ingredients until evenly distributed, but avoid overmixing. Use a rubber spatula to fold in chia seeds. Chill the batter in the fridge for 30 to 60 minutes.
- Stir the batter and then divide the batter between prepared muffin tins. Aim for ¾ the way full. Avoid overfilling.
- Bake at 350°F for 14-16 minutes.
- Allow them to cool in the pan for about 10 minutes before enjoying.
- Allow the lemon muffins to cool completely before drizzling them with powdered sugar glaze.
Storage
Storing: Allow the lemon chia seed muffins to cool completely. Once cool, store at room temperature in an airtight container or resealable bag. Enjoy within 5 days for best quality. To keep them fresh for a couple of days longer, refrigerate the muffins instead.
Freezing: For longer storage, you can freeze unglazed muffins for up to 1 month. Par-freezing them in a muffin tin for about 20 minutes before transferring them to a freezer-safe container will prevent them from sticking together.
Defrosting: Thaw frozen muffins in the refrigerator for a few hours, or microwave for a minute or two.
Serving Suggestions
These lemony muffins taste great with pretty much anything!
For breakfast or brunch, they pair well with a slice of potato crust quiche or egg muffins.
As a snack, you can’t go wrong serving them with a vanilla latte, cup of tea, or a smoothie!
Lemon Muffin Recipe FAQs
Yes, absolutely! As written, this recipe yields enough batter for 12 standard-sized muffins or roughly 36 mini muffins. Add enough batter to fill each well of the pan 3/4 full. The bake time for mini muffins is approximately 8-10 minutes. Check them at the 7-minute mark to prevent them from over-baking. It’s better to remove them from the oven slightly underbaked, because they will continue to cook as they cool.
Chilling the batter for 30 to 60 minutes results in fluffy, bakery-style muffins with high tops. If this step is skipped, the recipe will still work, but the lemon chia seed muffins will not rise as well.
Chilling the batter overnight produces the best domed top, but the batter shrinks and stiffens quite a bit because the chia seeds absorb a lot of moisture.
For other muffin recipes, check out our collection of Healthy Muffin Recipes!
Lemon Chia Seed Muffins
Ingredients
- ½ cup honey 160 g, 118 mL
- ½ cup plain Greek yogurt 125 g
- 2 large eggs room temp
- ¼ cup avocado oil
- 3 tablespoons lemon zest
- 2 tablespoons lemon juice
- 1 teaspoon lemon extract
- 1 teaspoon almond extract optional – can sub more lemon or vanilla
- 1 ½ cups oat flour 160 g
- 1 ½ teaspoons baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 2 tablespoons black chia seeds
Optional Lemon Glaze:
- ½ cup organic powdered sugar
- 1 tablespoon fresh lemon juice
Instructions
- Preheat the oven to 350℉. Line a 12-count muffin tin with paper or silicone liners and set aside.
- To a large mixing bowl, add the honey, Greek yogurt, eggs, avocado oil, lemon juice, zest, lemon extract, and almond extract. Whisk together until smooth.
- Add the oat flour to the wet ingredients and whisk until the flour is fully incorporated.
- Sprinkle in the baking soda, baking powder, and salt. Whisk together to evenly distribute. *Note: If the leaving is not evenly distributed, your muffins might rise unevenly. However, you also want to avoid over-mixing.
- Use a rubber spatula to fold the chia seeds into the batter. Just mix long enough to distribute and ensure there are no pockets of dry chia seeds. Do not over-mix.
- Chill the batter in the fridge for 30-60 minutes. *Note: This step can be skipped if you’re in a hurry, but it improves the texture and helps activate the baking powder so the muffins rise higher.
- After chilling, give the batter a quick stir, then use a cookie scoop or large spoon to divide the batter between the muffins wells. Aim to fill them ¾ full. Avoid over filling.
- Place the muffins in the preheated oven and bake for 14-16 minutes (15 minutes was perfect for my oven, but if you skip chilling the batter, they will cook faster so check at 12 minutes).
- Remove the muffins from the oven and allow them to cool for about 10 minutes before enjoying.
- Optional Lemon Glaze: Combine the powdered sugar and lemon juice in a small bowl and stir together until smooth. Drizzle on baked and fully cooled muffins.
Notes
- For the best flavor, use fresh lemon zest and lemon juice. 1 large lemon should yield enough zest and juice for this recipe.
- If you use melted coconut oil instead of avocado oil, you will want the yogurt and eggs to be room temperature. This prevents the coconut oil from solidifying.
- Mini Muffins: This recipe yields 12 regular size or 36 mini lemon muffins. Reduce the bake time to 8-10 minutes for mini muffins. Check them at 7 minutes to prevent them from over baking. Keep in mind that they will continue to bake out of the oven as they cool.
- Nutrition information does not include the optional glaze.
Absolutely delicious! First tried with almond flour but didnt get the rise. Oat flour worked best.
Do I use 118 mL of oil or a quarter cup of oil? one is twice as much as the other but both of those measurements are given for the one ingredient
¼ cup. Apologies for the confusion, I just updated the recipe.
These were amazing and delicious 😋 I would recommend putting on the icing! It was so good my family asked me for more!
Definitely 5 stars, love these! Make sure you don’t skip the step to chill the batter before baking.
Absolutely delicious! Great recipe for healthy, flavorful and moist muffins. Mine took an extra 5 minutes to fully bake.
I don’t have any gluten issues, could I use regular flour instead?
I have only tried this recipe with oat flour. I would recommend making it with oat flour as baking is a science!
I was so excited to make these. We can no longer find these in the store. They changed to a streusel topping which is not as good as a glaze. These taste identical, if not better. I will not be buying the box mix ever again and will absolutely will be making these regularly. The chemical reaction that happens is pretty cool too for all the science nerds out there.
I absolutely LOVE this recipe! These muffins are so moist and delicious we are now using them as a dessert with a dollop of fresh whipped cream.
Thanks to The Clean Eating Couple for so many easy and healthy recipes! They are my go to “cookbook” these days. I’ve never been much of a cook, but I can make these dishes.
Also, try their homemade dressing recipes. I will never buy a store-bought dressing again!
Can I substitute almond flour for the oat flour?
We covered this in the green substitutions section: Store-bought or homemade oat flour can be used. If using homemade oat flour, ensure the oats are processed into a very fine flour with no visible oats. Check out this post on making homemade oat flour for a full tutorial. If you need this recipe to be gluten-free, be sure to select gluten-free oat flour or gluten-free old-fashioned oats to make oat flour with. You can not use almond flour or coconut flour in place of oat flour.
Can you replace Oat Flour with Almond Flour?
We covered this in the green substitutions section: Store-bought or homemade oat flour can be used. If using homemade oat flour, ensure the oats are processed into a very fine flour with no visible oats. Check out this post on making homemade oat flour for a full tutorial. If you need this recipe to be gluten-free, be sure to select gluten-free oat flour or gluten-free old-fashioned oats to make oat flour with. You can not use almond flour or coconut flour in place of oat flour.
How do you go about baking 16 muffins since standard muffin tins have 12 or 6 “holes”?
bake 12, remove from the muffin tin, then bake the other 4.
Just made these this afternoon. They are delicious! I love that you can taste the lemon in them! Will definitely be making these again! They are also hubby approved!
This is such a great recipe. My family loves them every time I make them. I make them in as small muffins and add blueberries also (sometimes huckleberries – super small and delicious). Thanks for the recipe!!
So happy you liked them, Megan! Thank you!
Another great muffin recipe made this morning!! Thank you, Liz!!
So glad you liked them, Stacey!!
Really surprised at how fuffy they came out. SUPER simple to make — had all of the ingredients in my apt without having to search for anything crazy. Added collagen peptides to make them even extra special.
Really glad to hear you liked them Dani!! And that the collagen peptides addition worked out 🙂
Love love love these! My family devours them whenever I make them!
That makes me so happy to hear, Ali!! Love that your whole family loves them 🙂
I have a ton of chia seeds I need to find more ways to use, so I can’t wait to try this! Love a healthy muffin recipe.
Thanks girl! I can’t wait to try the pumpkin zucchini muffins you posted about!!
They look so perfectly peaked and really yummy; I love the fresh taste of lemons and poppy seeds in muffins.
It’s baking soda! My secret weapon 🙂 Lemons in any baked good are great!