Why These Muffins Beat the Bakery (or Store Bought)
If your mornings look anything like mine—toddlers negotiating breakfast while you juggle coffee and car seats—portable, nourishing muffins are a lifesaver.
This round-up pulls together 15 reader-tested healthy muffin recipes (many of them my own, a few from trusted friends) that sneak in fruit, veggies, fiber, and protein without loads of refined sugar.
Think banana-chocolate, pumpkin-oat, and even zucchini-double-chocolate—all sweetened naturally and sized for little hands.
Table of Contents
Here on What Molly Made I LOVE muffins. They’re one of my favorite things to bake. Whether your a meal prep muffin person, weekend baker, or need something for a school treat, this roundup of healthy muffins for kids is for you!
What Makes a Muffin Healthy?
- Whole-grain or grain-free flours (oat, almond, coconut, or 1:1 GF blends)
- Natural sweeteners like ripe bananas, applesauce, maple syrup, or honey
- Hidden produce—carrots, zucchini, spinach purée for bonus vitamins
- Better fats—avocado oil, coconut oil, or nut butter instead of butter sticks
- Smart add-ins—chia seeds, ground flax, or collagen peptides for protein
Pantry Staples for Anytime Muffins
| Category | Keep These Stocked |
| Flours | Almond flour, tapioca flour, coconut flour, GF 1:1, whole-wheat pastry, oat flour |
| Binders | Eggs or flax eggs, unsweetened apple sauce, Greek yogurt |
| Sweeteners | Bananas, canned pumpkin, maple syrup, coconut sugar |
| Fats | Coconut oil, avocado oil, nut butter, grass-fed butter |
| Mix-Ins | Mini chocolate chips, frozen berries, grated veggies, nuts |
15 Healthy Muffins for Kids
1. Chocolate Banana Blender Muffins (GF, DF)
Why Kids Love it: Double-chocolate flavor; made entirely in a blender—no bowls to wash.
2. Blueberry Lactation Muffins (Minus Brewers Yeast)
Why Kids Love It: Bakery-style crumb + antioxidant berries.
3. Gluten Free Pumpkin Muffins (GF, DF)
Why Kids Love It: Cozy spices + chocolate chips; perfect fall treat.
4. Paleo Cinnamon Streusel Carrot Cake Muffins (Paleo, DF)
Why Kids (& Grownups) Love It: Hidden carrots + crunchy crumb topping.
5. Mini Greek Yogurt Chocolate Chip Muffins (GF option)
Why Kids (& Grownups) Love It: Pools of chocolate, bite-sized + extra protein.
6. Healthier Lemon PoppySeed Muffins
Why Kids (& Grownups) Love Them: Bright citrus; reduced sugar glaze kids lick off first.
7. Low Carb Pumpkin Muffins (LC, GF)
Why Kids (& Grownups) Love Them: Almond-flour base keeps blood sugar steady.
8. Healthy Morning Glory Muffins
Why Kids (& Grownups) Love Them: Carrot-apple-pineapple trifecta; fiber-packed.
9. Almond Flour Chocolate Chip Muffins (GF, DF)
Why Kids (& Grownups) Love Them: Soft crumb, classic flavor, grain-free.
10. Chocolate Chip Oatmeal Muffins
Why Kids (& Grownups) Love Them:Fiber-packed oats, soft crumb + bakery-style tops.
11. Healthy Coconut Oil Gingerbread Muffins (DF)
Why Kids (& Grownups) Love Them: Holiday spice, no refined sugar.
12. Peanut Butter and Jelly Muffins
Why Kids (& Grownups) Love Them: Lunch-box favorite in muffin form.
12. Healthy Banana Muffins (DF, GF)
Why Kids (& Grownups) Love Them: )ne-bowl staple sweetened only with bananas & honey.
14. Healthy Pumpkin Muffins (GF, DF)
Why Kids (& Grownups) Love Them: Dump-and-stir convenience; freezer superstar.
15. Double Chocolate Zucchini Muffins
Why Kids (& Grownups) Love Them: Veggie stealth + brownie vibe—instantly kid-approved.
GF = gluten-free • DF = dairy-free • WF = whole-wheat • P = paleo • LC = low-carb • V = vegan
I hope you love these recipes as much as I do! Healthy muffin recipes are some of my favorite. If you love this round up or make one of these recipes let me know by following along on Instagram and tagging #WhatMollyMade.
Customizable Healthy Muffin Recipe
Save this Recipe!
Ingredients
- 1 1/4 cups gluten free oat flour
- 1/2 cup tapioca flour
- 1/2 cup ground flax seed
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 2 eggs
- 1/3 cup raw honey
- 1/3 cup unsweetened vanilla almond milk or coconut milk
- 2 tablespoons coconut oil melted and cooled
- 1 teaspoon vanilla extract
- Optional additions: cinnamon, diced apples, blueberries, bananas, cranberries, walnuts, peanut butter, nutella, lemon zest, poppy seeds
Instructions
- Preheat the oven to 350°F. Line 9-10 muffin cups with liners and spray the liners with nonstick cooking spray (I like coconut oil spray).
- In a small to medium bowl, whisk together the oat flour, tapioca flour, ground flax seed, baking soda and salt.
- In a separate large bowl, whisk together eggs, honey, vanilla, almond milk, coconut oil and lemon juice until smooth and well combined. Add dry ingredients to wet ingredients and stir until just combined.
- At this point, add whatever mix ins you have on hand like chocolate chips, blueberries, strawberries, apples and cinnamon or more.
- Use a large spoon to fill the prepared muffin liners all the way to the top, but not over the top. It should fill 9 to 10 muffin cups. Place a few extra blueberries on top of each one before baking. Bake in the preheated oven for 20-24 minutes or until a toothpick inserted comes out clean.
- Transfer muffin tin to a wire cooling rack and allow to cool for 5-10 minutes then remove the muffins from the tin and allow to cool completely or serve warm.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Parents Ask, Kids Snack
Cool fully, wrap each in parchment, store in an airtight freezer bag. Thaw at room temp or microwave 20 sec.
Aim for < 6 g added sugar per muffin; most recipes above fall under that when sized as minis.
Use sunflower-seed butter instead of nut butter and skip almond flour; sub oat or GF 1:1 flour instead.
Yes! Finely grate zucchini or carrots and squeeze dry; they disappear into chocolate or banana batters.
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