
Lemon Blueberry Greek Yogurt Muffins Recipe (Healthy & Gluten-Free!)
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These delicious and healthy lemon blueberry Greek yogurt muffins are a popular indulgence at Legacy Blueberry Farm when it’s picking season and fresh blueberries are available in abundance! Gluten-free and egg-free with substitutions available for vegan, paleo, and keto diets – these blueberry muffins come together in a pinch and are so fluffy, moist, and yummy, you won't be able to stop at just one – which is totally okay, because they are also good for you!

There’s nothing like waking up on a Saturday morning to the smell of blueberry muffins turning golden brown in the oven. With so many blueberry recipes available today, it can be hard to decide which recipe to make! Look no further, our famous Legacy Blueberry Muffin recipe is as tasty as it gets and is healthier than your average muffin.
What makes these blueberry muffins healthy?
Organic Blueberries
Blueberries are one of the healthiest fruits you can eat, especially when you select high quality, organic blueberries! They are filled with vitamins and minerals your body needs to thrive and contain tons of antioxidants (even more than green tea) that help fight against aging and cancer. Not to mention, one cup of fresh blueberries is only 80 calories and lower on the glycemic index than many other fruits. They add just the right balance of sweet and tart flavors and juicy goodness to your bakes while boosting heart health, mental health, improving digestion, and more – to learn all about the incredible health benefits of blueberries, check out our article here!
Organic Lemon
Lemons and blueberries just go together. A classic flavor pairing, the bright zingy flavor of lemon elevates the sweeter blueberry flavor in these lemon blueberry muffins for a mouthwatering summertime treat, meant to be enjoyed no matter the time of year! Lemons bring with them many health benefits of their own, including high amounts of Vitamin C and incredible detox and liver supporting properties.
Whole Food Sweeteners
Both raw cane sugar and raw honey are whole food sweeteners that are more efficiently processed by the body than refined sugar, which aids in more stable blood sugar levels. They also contain healthy trace minerals!
Raw cane sugar is a source of iron, potassium and other essential nutrients, while raw honey contains 22 amino acids, 27 minerals and 5,000 enzymes, along with important minerals and vitamins like iron, zinc, potassium, calcium, phosphorous, magnesium and selenium, vitamin B6, thiamin, riboflavin, pantothenic acid, and niacin. Sweet and health-boosting? Yes, please and thank you!
Plain Greek Yogurt
Greek yogurt is a great source of protein, healthy fats, calcium, and other nutrients. In addition to keeping you full longer, it helps keep these gluten-free blueberry muffins extra moist and fluffy!
A health benefit of having protein with your sugary treats is that protein supplies the body with amino acids which help to stabilize blood sugar and reduce cravings for carbohydrates. Meanwhile, the healthy fats found in Greek yogurt aid in the absorption fat-soluble vitamins, like Vitamin A, D, E, and K, as well as helping your body maintain its ability to burn fat for energy instead of just simple sugars and carbs – which helps you keep that fat off your waistline! It’s easy to see why we love using Greek yogurt in our healthy lemon blueberry muffins, isn’t it?
However, if you’re looking to cut fat and calories, feel free to substitute the plain full-fat Greek yogurt out with applesauce or a low-fat or plant-based yogurt. These muffins will still be totally delicious!
Grass-Fed Butter
Butter makes everything better, right? We think so! Not only is it delicious, grass-fed butter is nutrient dense, containing significantly more beneficial fatty acids than butter from grain-fed cows plus Vitamin A and antioxidant beta carotene. It’s also high in Vitamin K2, an important nutrient for heart and bone health. When it comes to baking, grass-fed butter is a simple and healthy substitute for oils, margarine, and commercial butter with lower proportions of healthy fats.

How to make our Famous Healthy Lemon Blueberry Greek Yogurt Muffins
These whole food sweet treats can be prepared in as little as 30 minutes, yielding 12 large individual muffins.
Scroll down for ingredient substitutions to make this recipe work with your unique dietary needs, including vegan, paleo, and keto variations.
Ingredients
- 2 cups gluten-free flour
- 1 TBS aluminum-free baking powder
- 1 teaspoon aluminum-free baking soda
- ½ cup raw cane sugar
- ¼ cup raw honey (omit if less sweetness is desired, but we love the bright summery flavor combination of honey, lemon, and blueberries!)
- 4 TBS (¼ cup) grass-fed butter, softened
- 1 TBS grass-fed butter or oil (to grease the pan)
- 1 cup Greek yogurt
- ½ cup organic & grass-fed milk (or dairy-free milk of choice)
- 1 organic lemon, grated and juiced
- 1 ½ cups fresh organic blueberries (frozen blueberries work as well, see note in instructions)
Instructions
- Preheat your oven to 375°F and grease your muffin tin with about 1 tablespoon of grass-fed butter or oil.
- Mix flour, baking soda, baking powder, and sugar in a medium-sized bowl.
- In a separate large bowl, whisk together the Greek yogurt, milk, and softened grass-fed butter.
- Zest the lemon and squeeze the juice into the mixture. Whisk to combine lemon juice plus zest with the rest of the wet ingredients.
- Combine dry and wet ingredients into one large bowl and stir together.
- Gently fold blueberries into the batter. (Note: If using frozen blueberries, keep frozen until right before you add them to your batter, and coat with a sprinkle of flour in a separate small bowl before folding into the batter to avoid streaking. If you don't mind purple muffin batter, then feel free to just toss them straight in.)
- Scoop batter evenly into the muffin tin. A large cookie scoop makes for nice, even muffins with round tops!
- Bake muffins for 20-24 minutes, until muffins start turning golden on top and a toothpick can be inserted inside the middle of the muffin and come out clean.
- Allow the muffin tin to cool on a cooling rack for 10 minutes, then remove the muffins from the tin and cool completely.
Share your muffins with friends, family, and neighbors!
Can I replace the Greek yogurt with sour cream in this muffin recipe?
If you've seen recipes online for sour cream blueberry muffins, or perhaps you have a tub of sour cream sitting in your fridge and you're curious if it will work the same way, the answer is yes! The flavor and consistency of sour cream is so similar to plain Greek yogurt that you can absolutely switch the out without noticing a difference in the end result.
Can I use dried blueberries in place of fresh or frozen?
Yes, you can use dried blueberries! When using dried blueberries for cooking or baking, soak in hot water for 5-10 minutes to rehydrate the blueberries. Drain thoroughly and coat with a bit of flour as you would with frozen blueberries before adding to your muffin batter.
How do I store my blueberry muffins?
These muffins can be stored in an airtight container at room temperature for up to 2 days and in the refrigerator for 5 days. If you have enough willpower to resist eating your muffins, they can even be stored for up to 2 months in the freezer!

Substitutions
We make these blueberry muffins gluten-free and egg-free, but you can really adjust the recipe to fit any diet by substituting out the dairy, sugar, and flour.
Make these muffins dairy-free & vegan!
Substitute the Greek yogurt with equal amounts of dairy-free yogurt, and for the milk use a dairy-free milk of choice.
You can also use applesauce in place of the yogurt and milk.
Replace the grass-fed butter with a plant-based butter or coconut oil.
Vegan Lemon Blueberry Muffin Recipe – Ingredients Variation:
- 2 cups gluten-free flour
- 1 TBS aluminum-free baking powder
- 1 teaspoon aluminum-free baking soda
- ½ cup raw cane sugar
- ¼ cup raw honey (omit if less sweetness is desired)
- 4 TBS (¼ cup) softened vegan butter or coconut oil
- 1 TBS oil (to grease the pan)
- 1 cup plant-based yogurt or applesauce
- ½ cup plant-based milk
- 1 organic lemon, grated and juiced
- 1 ½ cups fresh organic blueberries (see notes above for frozen or dried blueberries)
Make these muffins paleo!
Along with replacing the dairy with dairy-free alternatives mentioned above, you can make these muffins paleo by replacing the gluten-free flour with the following paleo flour blend instead. To make the blend, just mix all the ingredients thoroughly and store in a glass container. This blend will make more flour than you need, so just save the extra for your next paleo-friendly bake!
- 2 cups almond flour, sifted
- 1 cup arrowroot flour
- 1/2 cup coconut flour
- 1/2 cup tapioca flour or starch
Paleo Lemon Blueberry Muffin Recipe – Ingredients Variation:
- 2 cups paleo flour blend (see above)
- 1 TBS aluminum-free baking powder
- 1 teaspoon aluminum-free baking soda
- ½ cup raw cane sugar
- ¼ cup raw honey (omit if less sweetness is desired)
- 4 TBS (¼ cup) softened vegan butter or coconut oil
- 1 TBS oil (to grease the pan)
- 1 cup plant-based yogurt or applesauce
- ½ cup plant-based milk
- 1 organic lemon, grated and juiced
- 1 ½ cups fresh organic blueberries (see notes above for frozen or dried blueberries)
Make these muffins keto!
Yes, you read that correctly – you can even make these muffins keto-friendly! Simply replace the flour with 2 ½ cups of almond flour and 2 eggs.
Replace the honey and sugar with ½ cup Swerve Sweetener.
Use a little water to thin the batter out if needed, and omit the milk to further reduce carbs.
The plain full-fat Greek yogurt and grass-fed butter are definitely keto-friendly keepers in the original recipe!
Keto Lemon Blueberry Muffin Recipe – Ingredients Variation:
- 2 ½ cups almond flour
- 2 large eggs
- 1 TBS aluminum-free baking powder
- 1 teaspoon aluminum-free baking soda
- ½ cup Swerve Sweetener
- 4 TBS (¼ cup) grass-fed butter, softened
- 1 TBS grass-fed butter or avocado oil (to grease the pan)
- 1 ¼ cups Greek yogurt
- ¼ cup water, if needed to thin the batter
- 1 organic lemon, grated and juiced
- 1 ½ cups fresh organic blueberries (see notes above for frozen or dried blueberries)
Where can I find organic blueberries?
To enjoy maximum health benefits from your blueberries, it's always best to choose organic! Most grocery stores carry organic blueberries, but where is the fun in that? Come out to Legacy Blueberry Farm when it's blueberry season for all the blueberry-picking fun you can imagine! Our family-owned blueberry farm welcomes you with open arms.
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