20+ Healthy Muffin Recipes

A collection of delicious, dietitian-approved healthy muffin recipes that are perfect for breakfast, snacks, and even dessert! From classic morning glory and lemon poppyseed muffins to rich chocolate muffins, and even savory cornbread muffins, these easy muffin recipes are easy to make, nourishing, and perfect for the whole family.

It's no secret that I have a real muffin obsession. The proof is in all these fabulous recipes I've perfected over the years! Vegan muffins, gluten free muffins, flourless muffins, low sugar muffins...there's something for everyone.

I love the versatility of muffins (you can eat them any time of day!), that they keep me full and satisfied for hours, and that you can't beat the smell of baking muffins in your kitchen!

How to store muffins

Store homemade muffins in a tightly covered (or airtight) container at room temperature for up to three days, or in the refrigerator for up to five days.

Want to freeze? Simple freeze the cooled muffins on a lined baking sheet or plate. Once frozen, place them into a freezer bag and they'll stay fresh for up to three months.

When you're ready to eat, thaw them on the countertop, or warm them in the microwave individually!

Are homemade muffins good for you?

As a nutrition professional, my recipes have much less sugar and fat when compared to store-bought, bakery, or other traditional muffins. My recipes often include whole grains, nuts and seeds, fiber, and fruits or vegetables, all while limiting processed sugars.

I love to use healthy oils like avocado oil and coconut oil, plus unrefined sweeteners like maple syrup, honey or coconut sugar.

Many of the recipes in this round-up are also egg or dairy-free, gluten-free, or vegan! You can feel good about sharing these recipes with toddlers and kids because they're made with wholesome ingredients.

What flour is best for muffins?

It really depends on the recipe, but I like to use whole wheat flour (for the fiber!), whole wheat pastry flour (so fluffy!), or a combo of almond and oat flour for gluten free muffins.

You could also use half whole wheat flour and half all-purpose flour, or even 100% all-purpose flour if that's what you have on hand! Just check the "ingredients" and "substitutions" section of each recipe for more details on what flour will work best.

Helpful muffin tools

1. I love this muffin tin. Nothing sticks, so clean-up is a breeze.
2. This muffin pan comes with a lid if you need to transport your muffins.
3. A handy muffin scoop for easy and perfect muffin portioning.
4. Silicone liners or paper liners for easy clean up.

Healthy muffin recipes

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