Are you a muffin queen just like us? Here’s our favorite base muffin recipe for healthy muffins + 6 different healthy muffin recipes you can make with it!
Ultimate Muffin Recipe!
Grab a pen because you’re going to want to write down this base muffin recipe for our favorite healthy muffins. Today we’re sharing 6 unique muffin recipes with 1 classic 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 Variations
We have individual posts for each of these muffin variations, 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 Banana Nut Muffins
- Healthy Chocolate Muffins
- Cranberry Orange Muffins
- Apple Cinnamon Muffins
- Chocolate Pumpkin Zucchini Muffins
- Healthy Chocolate Chip Pumpkin Muffins

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. Feel free to sub light brown sugar 1:1.
- 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
Before we move into all of these delicious flavors, I thought we’d chat about substitution options for a second!
Substituations
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 would work as well as canola oil! If you try either of these, let us know how it works!
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!
What is the difference between a muffin and a cupcake?
Typically muffins are much more nutritious and contain less sugar. Cupcakes are typically made with white sugar and have frosting on top.
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.

Banana Base
Love healthy banana muffins? Take our classic muffin recipe and use mashed banana along with your other favorite add-ins to make the most delicious banana nut muffins or healthy chocolate muffins!
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)
Applesauce Base
Applesauce isn’t just for kids! Use our classic healthy muffins base and use a cup of applesauce for a slightly sweet and super moist addition. From there, make our cranberry orange muffins OR apple cinnamon muffins.
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

Pumpkin Base
Don’t let pumpkin muffins be an autumn-only treat! Our healthy pumpkin muffins base recipe is made with 100% pumpkin puree, making these muffins ever so sweet and moist as can be!
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.
Can You Freeze Muffins?
Muffins are a fantastic thing to freeze for later. Here’s a quick tutorial on how to do it:
- 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 Muffin Recipe (+ 6 Flavor Variations)
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.
I followed the recipe and made half apple cinnamon muffins, half banana and chocolate chip muffins. I added peanut butter to two of the banana chocolate chip muffins, just to experiment. Holy smokes, it was amazing! Great recipe, I will definitely be making more and next time I will make all banana, chocolate chip and peanut butter! Thanks 🙂
Look at those gorgeous muffins, Jennifer! Love that you split the batch into different flavors 😀
I’ve never been disappointed with a recipe from these – they’re always tasty, easy to follow, and a joy to make!
Banana Chocolate muffins and they both taste amazin
These are great!! Used whole wheat flour, left out the oil all together, used flax eggs and made the chocolate version. Huge hit with hubby and kids!!
I was looking for a muffin recipe for teacher appreciation brunch at my kid’s school. I found this easy recipe and made 3 different flavors – banana nut, pumpkin chocolate chip, and apple cinnamon. All three flavors turned out moist, distinct and delicious. In the photo from left to right are the banana nut, pumpkin chocolate chip and apple cinnamon. In hindsight I should have sprinkled nuts on top of the banana muffins for decoration instead of mixing them all into the batter. Maybe I also should have sprinkled chocolate chips on top of the pumpkin muffins. By take 3 – which was the apple muffins – I realized I needed to sprinkle rolled oats on top so the apple muffins would be distinguishable from the banana muffins. This was a great recipe and I will definitely use this again. Thanks!
I am wondering why you chose coconut oil with the HUGE amount of saturated fats in it? There was a coconut oil trend where people considered it “healthy” until people started realizing it’s packed with saturated fats and any positives are greatly outweighed by the negatives
. When using butter or margarine is it room temperature or melted to measure for a substitution? Other than the unhealthy coconut oil these look absolutely delicious! Thanks.
The outcome was fantastic! I don’t know whether anybody else has tried using “flax” as an egg substitute, but it worked well for us.
Thank you for sharing that a flax egg worked for you!
Not too sweet. I used gluten-free flour (which turned out great) but I thought it sounded like too much sweetener so I decreased the maple syrup a little…won’t do that next time. The amount she called for would be perfect!
Great muffins, good taste…however I noticed when I put them in tupperware box. After one night, muffins become humid (wet) on the top and sticky…do you know for what reason ?
There’s a lot of moisture in these so that’s likely the reason. Make sure they are totally cooled down before putting them in a container and don’t put the lid on tight so air can get in and out. I let muffins cool on the counter until pretty dry on top before storing or freezing.
Thanks for the advise !! will try to follow as you mentioned
they are simple to prepare and so delicious
Has anyone tried using self raising flour to get a bit more rise?
I just read to put a few saltine crackers in the container 😉
Hi, when you write 350deg or 180 Cdeg, do you mean both heaters or warm air?
Hi there1 I’m not sure what you mean by this. Set your oven to 350ºF!
These turned bout great! I am not sure if anyone else has used the “flax” instead of egg but we did and it turned out wonderful 💕
So glad your flax egg turned out! That is so good to note.
Can I substitute oat flour?
Hi! I think swapping 1:1 for oat flour would leave you with a super dense muffin. You could try 1/2 oat and 1/2 gluten-free or all-purpose?
Question: Do I use 1 cup pureed fruit PLUS the fruit mentioned in the varieties? For the apple muffins do I need 2 cups pureed fruit and 1 cup grated apples?
Just 1 cup total of pureed fruit! So 1 cup applesauce and 1 cup grated apples.
Thank you! Absolutely delicious. It might be helpful to make the amount of puree more clear in the recipe for everyone else!
My husband has a rare pumpkin allergy. What could we substitute the pumpkin for in the chocolate zucchini recipe? Applesauce? Thanks!
These are 1/2 cup banana ,blueberry Muffins ,.I did substitute applesauce for pumpkin in the chocolate ,zucchini recipe ..They are in the oven …
Cooked and pureed beets are a great choice in a chocolate muffin.
For those who don’t like the taste of Brown sugar I added Xylitol and it still tasted amazing
I have made these 2x and they are delicious! A great no-flour recipe! Thank you! Very yummy!
Not sure what I did wrong. I baked them for the amount of time stated and the inside were super mushy and not edible. Any tips?
That is very odd! Did you make any changes to the recipe? Specifically with what flour you used?
They surely are delicious but they’re not healthy 1 cup of sugars (maple and coconut) is too much calories adding the flour, etc. Thanks for the recipe (:
Will it be a matter if I cut the recipe by half?
I think you should be fine!
Do you think homemade Oat Flour will work as 1:1? Thank You!