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Healthy Breakfast Muffin Recipes

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I try very hard to eat healthy at every meal, but breakfast is my biggest challenge since I get tired of rotating between oatmeal, eggs, and yogurt. Every once in a while I want something convenient that I can grab on the way out the door.

So, I went in search of healthy breakfast muffin recipes that would offer me the convenience of a grab-and-go meal and would still be a healthy start to my day. I found dozens of great recipes and I’m sharing my favorite ones with you today.

a collage of eight different muffins with title text reading Healthy Breakfast Muffins

Gluten-Free Muffins

Since I recently switched to an anti-inflammation diet, I’ve tried to limit gluten, dairy, and sugar. So, I began my search by looking for gluten-free muffins. These four were my favorites.

These Cranberry Orange Muffins from Homemade for Elle are made with coconut flour (if you don’t have coconut flour try a substitute for coconut flour), avocado, and maple syrup in place of flour, butter, and refined sugar.

Cranberry-Muffin on a wire rack

These Low Carb Breakfast Muffins from Flour on My Face are made primarily with turkey sausage, cauliflower, and eggs resulting in a protein-packed portable breakfast.

Breakfast-Muffins on a white plate next to a glass of orange juice

I love veggie omelettes but don’t always have time to make one. These Veggie Omelette Bites from Divas Run For Bling are the perfect solution!

Veggie Omelette Bites on a white plate on a brown table

Quinoa is one of my favorite whole grains so I always have it on hand. These Quinoa Breakfast Muffins from Almost Supermom make good use of this superfood and with only 4 total ingredients, it’s easy to whip up a batch any time.

quinoa breakfast muffins on a plate with a glass of orange juice and a plate of sausage links in the background

Healthier Versions of Traditional Muffins

Of course, if you’re a carb lover, an egg-based muffin isn’t going to satisfy your craving. Thankfully, there are plenty of recipes that provide all the bread-y goodness of traditional muffins but with healthy swaps to make them much better for you and easier on your waistline.

These Clean Eating Blueberry Avocado Muffins from Divas Run For Bling swap out wheat flour for all-purpose flour, avocado for butter, stevia for sugar, and include greek yogurt for added protein and calcium.

blueberry avocado muffin on a white plate with a fork on it with title text reading Clean Eating Blueberry Avocado Muffins

These Skinny Pumpkin Protein Muffins also use whole wheat flour, but instead of adding greek yogurt for added protein, the recipe includes vanilla protein powder.

pumpkin protein muffins in a gray pan on a wood tale with title text reading Skinny Pumpkin Protein Muffins

I love the idea of switching up the traditional sweet, fruity muffins with something savory and these Zucchini Quiche Muffins from the Housewives of Frederick County are a perfect example of just how tasty a savory muffin can be.

Zucchini Quiche Muffins

Less Unhealthy Muffins

If you aren’t looking for a health-packed muffin that’s missing most of the ingredients you expect in a muffin, but instead want one you can enjoy with less guilt than a double chocolate muffin, you might enjoy one of these recipes.

These Cinnamon Apple Oatmeal Muffins from House of Faucis have equal parts oats and flour so you still get the texture of a regular muffin, but with the heart-healthy benefits of oats.

Cinnamon Apple Oatmeal Muffins in a green bowl with blueberries and banana slices with a basket of more muffins in the background and title text reading Cinnamon Apple Oatmeal Muffins

My Cranberry Walnut Muffins use a zero calorie sweetener in lieu of sugar and have phytonutrients from the cranberries and omega-3 fatty acids from the walnuts.

Cranberry Walnut Muffins on a wood background with title text reading Cranberry Walnut Muffins

These Strawberry Blueberry Muffins from Living Off Love and Coffee follow a very standard muffin recipe but are packed with antioxidants from the berries.

Strawberry Blueberry Muffins in a red dish next to more muffins, strawberries, and blueberries on a brown table

Make Your Own Healthy Muffin Recipe

The recipes above are all great ones to follow if you want to rely on a recipe that’s already been tried and tested. I encourage you to play with the recipes to include your favorite flavors. If you don’t like cranberries, substitute blueberries in the recipe. If you really love chocolate, throw some cocoa into a recipe or add some dark chocolate chunks. Have a sweet tooth? Use banana instead of avocado in the recipes above where avocado replaced the butter.

Better yet, take your own favorite muffin recipe and make some healthy swaps. Here are some suggestions and guidelines:

Substitutions for butter/oil

  • Avocado puree (1:1 ratio)
  • Mashed banana (1:1 ratio)
  • Applesauce (1:1 ratio)

Substitutions for all-purpose flour

  • Whole wheat flour (7/8 cup whole wheat = 1 cup all-purpose)
  • Coconut flour (use this chart to convert your recipe)
  • Oat flour (1:1 ratio) – you can make your own by putting oats in your blender (1/4 cup oats = 1 cup oat flour)

Substitutions for sugar

  • Low or no-calorie sweeteners like Splenda or stevia
  • Reduce sugar by half and add more vanilla extract
  • Honey or maple syrup (follow ALL of the guidelines below)
    • Use 1/2 cup to replace 1 cup of sugar
    • Reduce liquid in the recipe by 1 Tbs for every 1/4 cup
    • Add 1/2 teaspoon of baking soda per cup

Other swaps

  • If the recipe calls for buttermilk, substitute an equal amount of skim milk with lemon juice added to curdle it (let it sit for 5 minutes before adding the mixture to the other ingredients).
  • Whip egg whites and fold into the batter instead of using whole eggs. This will also lighten up the texture if you’ve used a heavier flour in place of all-purpose flour.
  • Use cacao nibs in lieu of chocolate chips.

Don’t want to mess with figuring out substitutions but still want the freedom to enjoy YOUR favorite flavors in a healthy breakfast muffin? Whip up this Healthy Breakfast Muffin Mix from The Sunny Patch and add whatever flavors you want. It’s gluten-free and sugar-free but still delivers a moist, fluffy muffin.

a measuring cup of muffin mix with a jar of muffin mix in the background, all on a brown table with title text reading Healthy Breakfast muffin mix

1 thought on “Healthy Breakfast Muffin Recipes”

  1. Oohhh, the veggie omelet bite muffins look delish! Can’t wait to work my way down your list of breakfast muffins. My family will be thrilled, too.


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