The Best Healthy Blueberry Muffins Recipe that is so easy to make! Learn how to make blueberry muffins with only 11 ingredients!

This post contains affiliate links. As an Amazon Associate I earn from qualifying purchases. Click here to read my policy and about affiliate links.
There are few things better than taking a big bite our of a fluffy blueberry muffin that is bursting with sweet blueberries.
Blueberry Muffins are the epitome of delicious breakfast treats right there next to pancakes. They’re soft, sweet, buttery and delicious… what’s not to love?

This recipe is perfect for those who want to indulge in the deliciousness of blueberry muffins without all the extra fat, sugar and calories.
This recipe has less than 150 calories per muffin, can be made gluten free, and is lower in fat/sugar when compared to your standard muffin. Here’s why we love it.
Why we love this Blueberry Muffin Recipe:
There are many reasons to love these healthy blueberry muffins and here are a few:
- Easy to make: These light and fluffy muffins use less than 15 ingredients (mostly pantry staples) and take just over 30 minutes to make!
- Low in sugar: This only added sweetener in these blueberry muffins is honey instead of the loads of refined sugar that many muffins have. Each muffin has 16g of all natural sugar.
- Low fat: Many muffin recipes use butter or canola oil to get moist muffins, but ours have a little olive oil, milk and apple to give you the most delicious and moist muffins while still being low fat! Each muffin has only 2g of fat.
Ingredients for Healthy Blueberry Muffins
To make these muffins, you will need:
- olive oil
- egg
- vanilla extract
- honey
- milk
- applesauce
- whole wheat flour OR oat flour
- cinnamon, nutmeg, ground ginger
- baking powder, baking soda
- fresh blueberries
We love these silicone muffin liners for baking!

How to make blueberry muffins?
Making easy blueberry muffins is so simple! Here’s how to do it:
- Preheat the oven to 350 + and prepare a lined muffin tin.
- In a large mixing bowl whisk olive oil, egg, vanilla extract, honey, almond milk and applesauce.
- Stir dry ingredients into wet ingredients until combined (whole wheat or oat flour, spices, baking powder/baking soda)
- DON’T over-mix. Let the batter sit for one minute.
- Fold in blueberries with a spatula.
- Pour batter into lined muffin tin, filling in ¼ cup increments.
- Bake at 350 for 20-25 minutes, or until the top of muffins are golden and a toothpick comes out clean when inserted in the center.
- Allow muffins to cool completely for at least 10 minutes, remove from pan + enjoy!





How long does it take to make homemade blueberry muffins? These homemade blueberry muffins are done in under 30 minutes start to finish!
Is it easy to make muffins? Yes! It’s so easy to make muffins. Even if you are a novice cook, you will easily be able to make these absolutely delicious muffins!
SUBSTITUTIONS FOR HEALTHY BLUEBERRY MUFFINS
Can the same recipe be used to make Gluten-Free Blueberry Muffins? Yes, just use gluten-free oat flour or another gluten free flour.
Olive Oil: You can substitute avocado oil, coconut oil, canola oil, or melted butter.
Egg: I haven’t tried making this with an egg substitute so I’m not sure if it would work.
Vanilla Extract: vanilla extract is optional and can be omitted.
Honey: You can substitute honey with maple syrup (1:1 ratio).
Milk: If you don’t want to use dairy milk, almond milk, cashew milk, or oat milk would work to make it dairy free.
Oat Flour: Oat Flour makes them taste like blueberry oatmeal muffins! You can substitute oat flour with whole wheat flour (1:1 ratio) and it will work great. You can also substitute with gluten-free oat flour. If you don’t have oat flour, follow this DIY Oat Flour Recipe. DO NOT substitute almond or coconut flour– It will not work.
Blueberries: We haven’t tried this recipe with frozen blueberries but I think it might work. I would recommend thawing the frozen blueberries and draining them before adding to the muffins. We haven’t tried substituting other berries in these muffins but I think blackberries or raspberries would work.
Banana: If you love bananas and blueberries, try our Banana Blueberry Muffins.
What do you eat easy blueberry muffins with?
How to serve healthy blueberry muffins: These muffins are great topped with peanut butter, on their own as a snack, or alongside a breakfast dish like sausage egg casserole.
Here are some other things you can serve with blueberry muffins:
- Potato Crust Quiche
- Chicken Breakfast Sausage
- Sausage Egg Casserole
- Sheet Pan Breakfast
- 5 Healthy Yogurt Parfaits
Is a muffin a good breakfast? Yes, these healthy blueberry muffins make a good breakfast! I recommend pairing them with yogurt or eggs for a higher protein breakfast that will keep you full.
Is a blueberry muffin a healthy snack? These muffins make a good snack! We recommend pairing a muffin with a Healthy Yogurt Bowl for a filling snack because you’ll need a little bit more protein to keep you full!

How do you store the best blueberry muffins?
Storing easy blueberry muffins: These muffins will last up to a week in the refrigerator. I don’t recommend storing them on the counter, because they can get moldy very quickly.
How to freeze healthy blueberry muffins: Yes, you can freeze these blueberry muffins. I recommend laying them flat in a reusable Ziploc bag and freezing them so that they don’t stick together. To defrost, microwave, or put them in a toaster oven.
How long does the homemade muffin last? Homemade blueberry muffins last for up to 1 week in the refrigerator or up to 3 months in the freezer.
Blueberry Muffin FAQ
The best way to keep blueberries from sinking to the bottom of muffins is to avoid over mixing your batter and gently folding in the blueberries. Some recipes call for adding 1/2 the batter to the tin, then adding blueberries, then adding the remaining batter but we don’t recommend this.
Your muffins may be soggy in the middle because they’re under done. Try baking them for a few more minutes.
Your blueberry muffins could be flat if your oven isn’t hot enough, or if you’ve over mixed your batter. Flat muffins could also be the result of expired baking powder or baking soda. Even if your muffins are flat they will still be delicious!

Other healthy muffin recipes:
We absolutely love healthy muffins! Check out these 30+ Healthy Muffins, or these:

Healthy Blueberry Muffins
Ingredients
- 1 tablespoon olive oil
- 1 egg room temperature
- 2 teaspoon vanilla extract
- 1/2 cup honey
- ¾ cup milk dairy or nondairy
- 3/4 cup applesauce
- 2 cups whole wheat flour OR oat flour
- 1 teaspoon cinnamon
- 1/4 teaspoon nutmeg
- 1/4 teaspoon ground ginger
- 1 1/2 teaspoons baking powder
- 1 teaspoon baking soda
- 2 cups fresh blueberries
Instructions
- Preheat the oven to 350 + and prepare a lined muffin tin.
- In a large bowl whisk together olive oil, egg, vanilla extract, honey, almond milk and applesauce.
- Stir dry ingredients into wet ingredients until combined (flour, spices, baking powder/baking soda)
- DON’T over-mix. Let the batter sit for one minute.
- Gently fold in blueberries with a spatula.
- Pour batter into lined muffin tin, filling in ¼ cup increments.
- Bake at 350 for 20-25 minutes, or until the top of muffins are golden and a toothpick comes out clean when inserted in the center.
- Allow muffins to cool completely for at least 10 minutes, remove from pan + enjoy!
Mary says
Simple and healthy recipe which result in a moist and tasty muffins. I used oat flour and the muffins came out light. I toasted and put butter on them as they are only 155 calories! Love your recipes.
Football season has started and your buffalo chicken dip is back on our menu. Thank you 🙏🏻
The Clean Eating Couple says
So glad you liked it, Mary! Thank you!
Sarah says
Very easy and delicious! Made into mini muffins and my toddler couldn’t get enough
The Clean Eating Couple says
So glad you liked them!
Alison says
Great recipe- I’ve made it twice. I used a combination of white whole wheat, oat and spelt flour. Only had 1/2 cup of applesauce so increased oil to 1/4 cup (avocado oil). Muffins have a wonderful texture, perfect sweetness and chock full of bluberries.
CW says
Can I use frozen blueberries?
The Clean Eating Couple says
We covered this in the blog post – Blueberries: We haven’t tried this recipe with frozen blueberries but I think it might work. I would recommend thawing the frozen blueberries and draining them before adding to the muffins. We haven’t tried substituting other berries in these muffins but I think blackberries or raspberries would work.
Sarah K says
So many people eat garbage on their way to work or school. These are much better that poptarts, which I stopped buying long ago! After reading you comment about pairing with eggs, I intend to pair them with the egg “muffins” that the family loves. (Muffins only because they are cooked in muffin tins.)
Though I’d prefer them to eat at the table but we can’t always achieve it so this could be an excellent alternative for THOSE days! Thanks for the recipe!
Sarah K says
Regarding the blueberries sinking, I have an old recipe that recommends rolling them in flour before adding them to the batter. This worked for me in that recipe.
Now, off to the store for some blueberries!
Penny says
Easy and delicious! My husband who loves his white sugar and flour even enjoys them.
JL says
Very good & super easy to make. Shared them with my prayer group who asked me for the recipe. I call that high praise. 🙂
Debbie says
Do you use unsweetened applesauce in this recipe?
The Clean Eating Couple says
I recommend using unsweetened to keep the sugar down. If you only have sweetened applesauce, I would use a little less honey 🙂