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.

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.

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.

1. Don’t overmix your batter.
2. In addition to oil, use pureed fruit for extra moisteness.
3. 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

1. Let your muffins cool compeltely.
2. Then, transfer them into an airtight container or gallon-size plastic bag (what we prefer to do!).
3. Remove as much air as possible and seal.
4. Freeze for up to 3 months.