Healthy Muffins (6 flavors)
Published 1/26/2024 • Updated 8/18/2024
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Are you a muffin queen just like us? Here’s our favorite base healthy muffin recipe + 6 different flavor variations!
These muffins call for simple ingredients you probably already have on hand and take just under 40 minutes to make from start to finish.
Ultimate Healthy Muffin Recipe!
We are muffin people and so are our kids! They make for the perfect quick snack and I almost always have a dozen on my counter or in my freezer. Today we’re sharing 6 unique healthy muffin recipes that all stem from 1 base recipe. You read that right. In this post, you’re going to get not 1, not 2, but 6 different healthy muffin recipes.
This isn’t an ordinary muffin recipe. It’s one that’s made with whole grains and better-for-you ingredients. Plus, these muffins come out super fluffy and pretty much taste like dessert.
The 6 Muffin Flavors
Since we’ve published this post, we’ve created individual posts for each of these healthy muffin variations because they were so popular! So, feel free to use the links below to go directly to the recipe you’re looking for. Or, head down to the recipe card for the muffin base + add-in directions.
Healthy Muffins – Base Muffin Recipe
First and foremost, let’s chat about our signature healthy muffins recipe. For all 6 of these healthy muffin flavors, you’ll notice that we used the same exact base recipe and then deviated slightly for each flavor.
We’ve tested this base recipe time and time again and let me tell you, it just works! Here’s what you need:
Dry Ingredients
- White whole wheat flour: we love cooking with white whole wheat flour and prefer to use the brand King Arthur. Your muffins will come out super light and fluffy.
- Coconut sugar: coconut sugar is one of two sweeteners in this recipe. We’ve also tested these muffins with light brown sugar as a 1:1 sub.
- Baking soda: baking soda helps make your muffins super fluffy!
- Salt: salt brings out the lovely add-in flavors.
Wet Ingredients
- Eggs: eggs help bind this muffin recipe together and also make them nice and fluffy.
- Maple syrup: maple syrup is the second sweetener used in these muffins. It’s a warm flavor and refined sugar-free!
- Unsweetened almond milk: we prefer to use almond milk, but any kind will do!
- Melted coconut oil: we love baking with coconut oil. Make sure to measure your coconut oil from the melted state to get an accurate measurement.
- Pureed fruit: pureed fruit is definitely what maeks these muffins so unique and delicious.
quick note!
You’ll note that each of these healthy muffin recipes calls for the same exact dry ingredients. When it comes to wet, they call for the same ingredients minus the pureed fruit.
Each of the 6 recipes will slightly differ, but the three pureed fruits we feature are: banana, applesauce, and pumpkin. The great thing about pureed fruit is that it will:
- add a serving of fruit to your muffins
- make your muffins super duper moist
Ingredient Substitutions for Healthy Muffins
White whole wheat flour: While whole wheat flour definitely works the best time and time again, but if you’re hoping to swap for a different flour, we suggest the following (and only the following) at a 1:1 ratio:
- all-purpose flour
- whole wheat flour
- all-purpose gluten-free flour blend.
Unfortunately, we do not recommend substituting 1:1 for coconut flour and/or almond flour.
Coconut sugar: The only sugar we would recommend swapping for coconut sugar 1:1 is light brown sugar.
Eggs: We have not tested these recipes without eggs. If you do try these recipes with a flax egg, please let us know how it goes!
Maple syrup: Honey would be a fantastic 1:1 swap for maple syrup, and potentially agave nectar.
Almond milk: Good news! Any kind of milk will work with a 1:1 swap. Try soy milk, cow’s milk, or coconut milk.
Coconut oil: While we haven’t tested any other subs, we’re confident butter, olive oil, and canola oil would also work.
What is the secret to making moist muffins?
We have a few tricks up our sleeve to making moist muffins.
- Don’t overmix your batter.
- In addition to oil, use pureed fruit for extra moisteness.
- Don’t over bake!
Which oil is best for muffins?
In our opinion, coconut oil is best for muffins because it’s light and doesn’t have a super-strong flavor. Others will say that vegetable oil or butter is best.
Healthy Banana Nut Muffins
These banana nut muffins are made with mashed banana, walnuts, ground cinnamon, and vanilla extract making them slightly spicy, good-for-you, and a great breakfast muffin recipe!
- 1 cup mashed bananas
- 1/2 cup walnuts, chopped
- 1 teaspoon ground cinnamon
- 1 teaspoon vanilla extract
Healthy Chocolate Muffins
If you like chocolate you’re going to love our healthy chocolate muffins! They’re sweetened with mashed banana and made with chocolate chips and cocoa powder to make them extra chocolatey and delicious.
- 1 cup mashed bananas
- 1/2 cup unsweetened cocoa powder
- 1/2 cup chocolate chips
- 1 teaspoon vanilla extract
- 1/4 cup almond milk (in addition to base recipe)
Cranberry Orange Muffins
With just a little bit of orange extract, orange zest, and dried cranberries, you’re going to get the most delicious cranberry orange muffins out there. Bonus…they’re healthy and 100% whole grain!
- 1 cup applesauce
- 1/2 teaspoon orange extract
- 1 tablespoon orange zest
- 2/3 cup dried cranberries
Apple Cinnamon Muffins
There is nothing better than a moist apple cinnamon muffin recipe. Made with applesauce, shredded apples, ground cinnamon and vanilla extract, these are a muffin all will love!
- 1 cup applesauce
- 1 cup shredded apples (moisture removed)
- 2 teaspoons ground cinnamon
- 1 teaspoon vanilla extract
Chocolate Pumpkin Zucchini Muffins
Made with both pumpkin and zucchini, these healthy chocolate pumpkin zucchini muffins are EXTRA moist and double the healthy with 2 servings of veggies.
- 1 cup pumpkin puree
- 1/2 cup cocoa powder
- 1 cup shredded zucchini (moisture removed)
- 1/4 cup almond milk, unsweetened (in addition to base recipe)
Healthy Chocolate Chip Pumpkin Muffins
What is better than pumpkin muffins? Chocolate chip pumpkin muffins! This recipe comes out so moist, has a hint of cinnamon, and is topped off with chocolate chips.
- 1 cup pumpkin puree
- 1 teaspoon vanilla extract
- 1 teaspoon ground cinnamon
- 1/2 cup chocolate chips
How to Store Muffins
Let your muffins cool completely. Then, transfer them into an airtight container. Store them in a cool, dark place such as your counter for around 3 days.
For best results, store these muffins in the fridge for up to 3-5 days. Since they have pureed fruit in them and are made with real ingredients, they are more apt to mold quicker on the counter.
How to Freeze these Healthy Muffins
- Let your muffins cool compeltely.
- Then, transfer them into an airtight container or gallon-size plastic bag (what we prefer to do!).
- Remove as much air as possible and seal.
- Freeze for up to 3 months.
Healthy Muffins (6 ways!)
Ingredients
Base Dry Ingredients
- 1.5 cups white whole wheat flour
- ½ cup coconut sugar, or light brown sugar
- 1 teaspoon baking soda
- 1/8 teaspoon salt
Base Wet Ingredients
- 2 large eggs
- 1/2 cup maple syrup
- 1/2 cup unsweetened almond milk
- 3 tablespoons melted coconut oil
- 1 cup pureed fruit*
Instructions
- First, preheat oven to 350ºF and line a muffin tin with muffin liners. We suggest also spraying your muffin liners with cooking spray just in case.
- Next, place dry ingredients into a medium bowl and mix.
- Then, in a large bowl crack 2 eggs and whisk. Add maple syrup, almond milk, and preferred pureed fruit* and mix again.
- Add dry ingredients into wet ingredients and then mix. Then, add in melted coconut oil and mix again.
- At this point, add any of the add-ins for one of the 6 muffin recipes in this post and mix again.
- Fill each muffin about 3/4 of the way full (these are going to be big muffins). Then, place in the oven at 350ºF and bake for 18-22 minutes or until the center is fully cooked.
- Let cool for 5 minutes and then remove from the muffin tin to continue cooling.
Tips & Notes
- Pureed fruit: the pureed fruit you use is dependent on which muffin recipe you are planning on using.
- Nutrition information includes 1 cup of unsweetened applesauce as the pureed fruit.
Watch It
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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Can anyone suggest tips for making these at high altitude (I live at ~4700ft)? I’ve made several attempts at altering the recipe on my own but I’m no chef! I’ve tried adding a bit more flour, more milk, less baking soda, you name it, but it’s coming out undercooked (and spongy even without overstirring) inside and near burnt outside cooking it at the suggest temp for 20mins.
High altitude baking is all about trial and error. This recipe seems to be fairly high in sugar (3 types used when counting the fruit purée) which at altitude leads to a quick rise and collapse, and hen a very dense center. Try reducing the sure by a tablespoon or two. It also sounds like your muffins suffered from low moisture (also another common problem at altitude. Try adding an extra tablespoon or two of moisture ( not fatty moisture – fat causes its own problems). Finally if you muffins did collapse, try using less parking powder/soda.
I raised 3 kids with multiple food allergies, sometimes you just need to pick a recipe and make it multiple times, making small adjustments until you get it the behaving properly! Good luck, enjoy what you learn!
Made Banana Nut muffins exactly as written in my standard size muffin tins and it made 18. They were delicious!! I did wonder if I wanted to up the protein by adding 1-2 scoops of vanilla protein powder what ingredients should I decrease or increase?
I’d add max 1/4 cup of protein powder. Decrease the flour by 1/4 cup!
I made the chocolate muffins with banana and I used all-purpose flour as I have been unable to find WW flour, let alone White WW flour (if any one knows what stores carry it lmk!) The batter would have been perfect for WW flour as it was very runny when using All purpose :(. I ended up baking for 28-29 minutes when the toothpicks finally came out clean. I reccommend either uping the all purpose flour to have a less runny batter or baking for longer like I did. Though I was pretty nervous the muffins were not going to peak, they did! The muffins taste amazing and I can’t wait to try the WW flour next time!
Oh and this recipe actually yeilded 20 muffins for me… I am wondering what size (depth and diameter) your muffins tins are to yeild 12? My tins are about 1 inch depth and 2.75 inches diameter for reference
Hi. I just read your post. I live in Canada, and I can’t find white ww flour, either. I believe it’s not available for us here. Maybe it’s the same where you live….just a thought.
I cannot find the flour either! I checked everywhere! Any suggestions? Does plain whole wheat work?
I thought Bob’s Red Mill used to carry this. They are out of stock on whole wheat pastry flour now unfortunately. That would probably work. King Arthur Flour is another brand . Try their websites or Fred Meyer/Kroger or Target maybe?
These are amazing! Thank you, for sharing the recipes so we can all eat a little healthier.
I’ve tried many other recipes for healthy muffins, but nothing compares to this recipe.
Grateful!!!
Hello, I am a little confused. If I make chocolate chip pumpkin muffins, am I adding 1 cup of pureed fruit to the wet ingredients PLUS 1 cup of pumpkin puree along with the extra ingredients, or is that 1 cup of pumpkin puree meant to be the 1 cup of pureed fruit you first mention in the wet ingredients part? Thank you.
Hi! The 1 cup of pumpkin is the pureed fruit you should use!
Thank you! I made the banana recipe and they were delicious. I’ll be trying the rest out over the next few weeks. Cheers.
Hi! Could I substitute the milk with Greek yogurt?
We haven’t tried this, so I can’t say for sure!
Great…..
Can you use apple sauce instead of coconut oil? Or half and half?
I don’t see why not!
I made the chocolate, banana, and the apple. These r amazing honestly better than the regular ones. U can’t tell there’s whole wheat at all
YAY! We’d love it if you could give us a star rating!
Thank you for sharing
My grandsons love to bake
And this has six options
There are three boys