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Muffins are the perfect bite-sized snack for kids, but many of the store-bought options are packed with sugar and other additives. These healthy muffin recipes for kids are made with wholesome ingredients you can feel good about, like whole grains, fruits, veggies, and more. Freeze the extras for later for easy grab-and-go snacks anytime!

A collage of eight healthy muffins for kids.

Make Ahead Healthy Muffins for Kids

As a registered dietitian and mom, I understand how important and challenging it is to feed your kids nutritious meals and snacks everyday. One of my favorite tips is to prep ahead wherever possible!

If you can make a single or double batch of any of these muffins and freeze them, you’ll have nutritious, unprocessed snacks on hand for any moment. This is ideal for when you need something to serve with breakfast or a healthy treat to tuck into their lunch boxes!

If you’re all about the make-ahead life (or you want to be), grab a copy of my ebook Healthy Little Bites for 40 of my most popular make-ahead snacks for kids!

Why You’ll Love These Healthy Toddler Muffins

  • Dietitian-formulated to be higher in fiber and healthy fats
  • Naturally sweetened with fruits, honey, or maple syrup
  • Freezable for easy snacks any time
  • Allergy-friendly options to accommodate different needs
  • Sweet and savory muffin options to serve with any meal
  • Made with nutritious ingredients to support your child’s overall health

Sweeter Muffins for Kids

ABC Muffins

ABC stands for apple, banana, and carrot, which gives these muffins the most wonderfully moist texture and sweet flavor!

ABC muffins in a white bowl on a table.

Mini Chocolate Chip Muffins

These are a must-have for the lunch box! They’re a healthier alternative to Little Bites and use white whole wheat flour for extra fiber. Plus, they’re sweetened with applesauce, so there’s no refined sugar (apart from the mini chocolate chips)!

Mini chocolate chip muffins stacked on top of one another in a white bowl on a plate.

Mini Blueberry Banana Muffins

These mini blueberry muffins are done in just 20 minutes and are made with almond flour for extra fiber, protein, and healthy fats. There’s also no added sugar! Great for kids!

Two mini blueberry banana muffins stacked on top of one another on a small white plate.

Mini Sweet Potato Muffins

The warm spices and roasted sweet potatoes give these homemade muffins a cozy fall flavor.

A mini sweet potato muffin with a bite taken out of it on a table, with muffins in the background.

Healthy Banana Muffins with 2 Bananas

Banana bread is a classic option, and this healthier alternative uses almond flour, making these muffins rich in healthy fats and naturally gluten-free.

Banana bread muffins stacked on top of one another in a decorative bowl on the table.

Carrot Zucchini Muffins

Don’t worry about your kids turning up their noses at the sight of green stuff in their muffins. These carrot zucchini muffins have plenty of sweetness from dried dates and are so tender and moist! 

A birds-eye view of carrot zucchini muffins on parchment paper.

Banana Blackberry Oatmeal Muffins

Blackberries add a tart flavor that balances the sweetness of the mashed banana and maple syrup. One of our favorites!

Two banana blackberry muffins stacked on top of one another.

Green Monster Muffins

If you have a picky eater who won’t eat their veggies, try these healthy spinach muffins! They’re sweetened with overripe bananas and applesauce, which also makes them moist and tender. We like to call them “hulk muffins” to get those picky eaters extra excited to eat them!

Green monster muffins in a polka dot bowl on a dining table.

3-Ingredient Banana Oatmeal Muffins

These peanut butter banana muffins are one of my favorite muffin recipes! They’re made with peanut butter, oatmeal, and mashed bananas, so they’re naturally gluten-free and egg-free. Plus, they’re loaded with fiber and healthy fats to energize them all morning long!

3 ingredient banana oatmeal muffins aligned on a polka dot plate.

Healthy Date Muffins

Dates add the perfect caramel-like sweetness to any muffin, and this easy muffin recipe showcases that natural sweetness incredibly well.

A bowl of healthy date muffins in a white bowl on top of a decorative plate.

Banana Blueberry Oatmeal Muffins

The combination of blueberry and banana always works, and the oats make these muffins extra hearty and satisfying. In fact, oats are a fantastic source of fiber, which can support your child’s digestive health, blood sugar levels, and heart health. They may also help them feel full for longer, which means they won’t be asking for another snack in 30 seconds.

Three banana blueberry oatmeal muffins stacked on top of each other.

Healthy Carrot Pineapple Muffins

If your kids like carrot cake, then these carrot cake muffins will taste like dessert for breakfast! They’re just sweet enough with warm spices, pineapple pieces, and homemade cream cheese frosting on top!

3 carrot pineapple muffins stacked on top of one another with the top one with a bite taken out of it.

Mini Strawberry Muffins

There are lots of reasons to love these little muffins, like the pops of fresh strawberries and the moist texture, but the very best part is that one batch makes 24 mini muffins! That’s plenty to enjoy a snack or two now and to freeze a bunch extra for later. 

A half-bitten mini strawberry muffin on top of another muffin on a small plate.

Gluten-Free Apple Muffins

Fresh apples, cinnamon, and maple syrup taste like fall in these flourless apple muffins! Plus, each one has 4g of fiber and 14g of fat to keep your kids full for a while.

A hand holding a gluten-free apple muffin with a bite taken out of it.

Flourless Peach Muffins

Fresh peaches add a pop of summer flavor that tastes delicious with the almond flour base. Totally irresistible!

Overhead image of gluten-free peach muffins on parchment paper.

Banana Protein Muffins

Kids don’t require nearly as much protein as adults, but if you have a hard time getting your kid to eat meat or eggs, these protein-packed muffins can be a great option to incorporate. The Greek yogurt adds a little extra, too.

Banana protein muffins on a blue plate.

Mini Almond Butter Muffins

The combination of almond butter and sweet dates gives these muffins a nutty caramel flavor my kids love. Plus, they’re bite-sized, so you only need 1 or 2 for a snack!

A bowl of mini almond butter muffins.

Honey Bran Muffins with Applesauce

I know the word “bran” doesn’t sound exciting, but hold your judgment until you try them! I’ve designed this great recipe to be sweet and moist with coconut sugar, honey, and applesauce. I also add orange zest for a refreshing aroma that makes them even more tempting. Both of my kids enjoy them!

Honey bran muffins in a tray with a bite taken out of one.

Mini Cornbread Muffins

Cornbread muffins tend to bridge the line between sweet and savory, and this option has just enough sweetness from honey. They use regular whole wheat flour, almond flour, and cornmeal for lots of fiber and healthy fats, and the honey cornbread flavor is just as delicious with leftover chili as it is with breakfast. 

Mini cornbread muffins stacked on top of each other in a bowl.

Pumpkin Oatmeal Muffins

Pumpkin puree is a fantastic ingredient for kids, as it’s high in beta carotene, potassium, and fiber. The dark chocolate chips add plenty of sweetness and make them taste decadent!

Three pumpkin oatmeal muffins stacked on top of each other.

Raspberry Banana Oatmeal Muffins

Made with rolled oats and oat flour, these oatmeal muffins are more like baked oatmeal than regular muffins. They’re a great way to serve your kids extra fiber and are a fantastic option for make-ahead breakfasts. The pop of raspberries takes them over the top!

A hand holding up a raspberry banana oatmeal muffin.

Savory Muffins

Veggie Quinoa Muffins

Cheese makes anything taste better, including fresh veggies and quinoa! These are the perfect make-ahead option for a quick lunch or dinner side dish.

Baked quinoa veggie cups stacked on top of one another on a stack of small colorful plate.s

Mini Egg Bites

Eggs are a great option for a nutritious breakfast, and this version has cottage cheese for extra creaminess and protein. Plus, they’re made with extra veggies to sneak in some fiber and nutrients!

Mini egg bites with cottage cheese and veggies on a white plate on the table.

Zucchini Frittata Muffins

Zucchini + eggs + cheese = yummy, kid-friendly muffins. Make a batch once on the weekend and serve them for a healthy breakfast all week long!

Zucchini frittata muffins in the shape of a heart on a colorful striped plate.

Crustless Mini Quiches

Made with bacon, chives, and plenty of cheese, these easy muffins are an ideal breakfast option even the pickiest kids will love.

Mini crustless quiches stacked on top of each other.

Turkey Sausage Egg Muffins

For a meaty option, try these sausage-filled egg muffins. They’re also made with spinach for extra greens, but the breakfast sausage links give them a deliciously savory flavor!

Two turkey sausage egg muffins on a plate with sweet potato hash.

Turkey Meatloaf Muffins

Although most of the recipes on this list are best for breakfast, these meatloaf muffins are perfect for lunch or dinner! They’re made with a mixture of ground turkey, apple, Dijon, and more, so they have a lighter flavor than traditional meatloaf.

A stacked of mini turkey meatloaf muffins.

Chicken Zucchini Poppers

These poppers are made by making ground chicken in muffin cups with shredded zucchini, spices, and fresh parsley. The spices give the muffins great flavor, and they’re the perfect shape and size to stash in those lunch boxes.

Chicken zucchini poppers aligned on a decorative blue and white plate.

Chicken Avocado Poppers

This easy recipe is a must-try for kids of all ages, but especially babies and toddlers! The avocado adds a creamy texture and healthy fats young kids really need.

A half-bitten chicken avocado popper on top of a whole one on a white plate.

Easy Chicken Muffins

These mini meatloaf muffins are such a great idea for a warm school lunch! The tomato sauce and melty cheese make them a hit with the whole family, too. 

A half bitten chicken muffins in parchment paper on a plate.
Healthy little bites book cover.

healthy little bites

 Ready to start making your kid’s snacks? This ebook has 40 of my favorite make-ahead healthy kid’s snacks and meals! They are all kid-tested and formulated by a dietitian and are much healthier than the processed snacks at the store!

Like it? Save the recipes for later!

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