Healthy Lemon Chia Seed Muffins are the perfect breakfast! They’re loaded with fiber, omega-3 rich chia seeds, low in sugar and gluten free!
If you’re looking for a healthy and delicious breakfast, Lemon Chia Seed Muffins are for you!
These simple muffins are packed with omega-3 fatty acids. Made with simple pantry staples, these muffins are low in sugar and gluten free – a great way to start your day.
Plus, they’re super easy to make!
What makes these muffins healthy?
- Healthy whole grains :The base of these muffins is a combo of oat flour. Usually, muffins are made with white flour, but the whole grains help make this a healthier muffin that will keep you fuller for longer!
- Low sugar: Rather than loading these muffins up with sugar, I sweetened them with honey!
- Nutrient Packed: Each muffin has 3 grams of fiber, 4 grams of protein, and 32% of your daily value for omega-3s.
Ingredients for Lemon Muffins
To make these lemon chia muffins you’ll need:
- honey – we like this to sweeten baked goods
- Greek yogurt – helps to add protein and moisture to the muffins
- eggs
- avocado oil – muffins need fat, and avocado oil helps give them the perfect texture
- lemon zest & lemon juice
- lemon extract, almond extract – the combo of lemon and almond extract gives these muffins such a delicious flavor
- oat flour – we love muffins made with oat flour – they’re moist and delicious!
- baking powder + baking soda
- salt
- black chia seeds – you could use poppyseeds too!
It will also be 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!
Substitutions for these Healthy Lemon Chia Seed Muffins:
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!
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 – 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.
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 also rises best when the batter is chilled because it allows the baking powder to activate before baking.
Black Chia Seeds – Black chia seeds are used in this recipe for a healthier spin on classic lemon poppyseed muffins. White chia seeds may also be used but aren’t as pretty. Poppyseeds will work similarly in this recipe and can be substituted 1:1 for chia seeds.
Gluten Free: If you want to make these muffins gluten free, make sure to use gluten-free oat flour. Oats themselves do not contain gluten, but they are generally processed on equipment shared with other gluten-containing grains and 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.
Tips for the best Healthy Lemon Muffins:
- When measuring the oat flour, be sure to use the “spoon and level” method to prevent overpacking.
- For this recipe, adding the oat flour to the wet ingredients and mixing well allows the oat flour to absorb some of the moisture and get fully incorporated into the batter before the leavening agents are added (which prevents over activating the leavening).
- 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 test chilling overnight. This produced the best domed top, but the batter did shrink and stiffen quite a bit because the chia seeds absorbed 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.
- Silicone muffin liners were tested and worked for this recipe. They do take just a minute or two longer to bake with 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.
How to Make Lemon Chia Muffins
- Whisk wet ingredients together until smooth. Whisk in the oat flour until fully incorporated. Then, whisk in baking soda, baking powder, and salt until evenly distributed, don’t overmix. Use a rubber spatula to fold in chia seed without overmixing. Chill the batter in the fridge for 30-60 minutes.
- Stir the batter and then divide the batter between prepared muffin tins. Aim for ¾ the way full. Avoid overfilling.
- Bake at 350° for 14-16 minutes.
- Allow them to cool for about 10 minutes before enjoying.
How to store lemon chia muffins:
Storing: Allow these Lemon Chia Seed Muffins to fully cool and then store in an airtight container or resealable bag at room temperature. Enjoy within 5 days for best quality. You can store them in the refrigerator to last longer.
Freezing: For longer storage, you can freeze the muffins for up to 1 month. It is helpful to par-freeze the muffins in a muffin tin for about 20 minutes to prevent them from sticking together, then transfer them to a resealable freezer bag, seal, and pop in the freezer.
Defrosting: Leave out the night before in the fridge and they will thaw out. Or – just pop it in the microwave for 1-2 minutes!
what to serve with lemon muffins
These lemon chia seed muffins are perfect for a quick breakfast or healthy brunch. They’re light, lemony, and go with pretty much anything!
You can pair these muffins with a slice of potato crust quiche, chia seed pudding, or egg muffins for breakfast. They also go well with a vanilla latte or pumpkin spice latte!
Try these other healthy muffin recipes!
For more muffin recipes, check out these 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 118 mL
- 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 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 2 tablespoons black chia seeds
Optional Lemon Glaze:
- 1/2 cup organic powdered sugar
- 1 tablespoon fresh lemon juice
Instructions
- Preheat the oven to 350 F. Line a 12-count muffin tin with paper or silicone liners and set aside.
- In a large mixing bowl, combine the honey, Greek yogurt, eggs, avocado oil, lemon juice, zest, lemon extract, and almond extract. Whisk together until smooth. (Note: if you use melted coconut oil instead of avocado oil, you will want the yogurt and eggs to be room temperature before combining to prevent the coconut oil from solidifying).
- 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. If the leaving is not evenly distributed your muffins might rise unevenly, but you also want to avoid over-mixing.
- Use a rubber spatula to fold the chia seeds into the batter. Just mix 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. This step can be skipped if you’re in a hurry, but it improves the texture and helps activate the baking powder, and the muffins will not have as much of rise without it.
- After chilled give the batter a quick stir and then use cookie scoop or large spoon to divide the batter between the muffins wells. Aim for ¾ the way full. Avoid over filling.
- Place the muffins in the 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 muffins when they are fully baked and cooled.
Berni says
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.
Kathleen Ashline says
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!
Penny says
Can I substitute almond flour for the oat flour?
The Clean Eating Couple says
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.
Carla says
Can you replace Oat Flour with Almond Flour?
The Clean Eating Couple says
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.
Old Grey Mare says
How do you go about baking 16 muffins since standard muffin tins have 12 or 6 “holes”?
The Clean Eating Couple says
bake 12, remove from the muffin tin, then bake the other 4.
Gail Hissom says
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!
Megan says
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!!
The Clean Eating Couple says
So happy you liked them, Megan! Thank you!
Stacey says
Another great muffin recipe made this morning!! Thank you, Liz!!
The Clean Eating Couple says
So glad you liked them, Stacey!!
Dani says
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.
The Clean Eating Couple says
Really glad to hear you liked them Dani!! And that the collagen peptides addition worked out 🙂
Ali Baldwin says
Love love love these! My family devours them whenever I make them!
The Clean Eating Couple says
That makes me so happy to hear, Ali!! Love that your whole family loves them 🙂
Jenna @ A Savory Feast says
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.
The Clean Eating Couple says
Thanks girl! I can’t wait to try the pumpkin zucchini muffins you posted about!!
Emily says
They look so perfectly peaked and really yummy; I love the fresh taste of lemons and poppy seeds in muffins.
The Clean Eating Couple says
It’s baking soda! My secret weapon 🙂 Lemons in any baked good are great!