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Breakfast has quickly become my favorite meal of the day! Between my 3 ingredient protein pancakes, gluten-free bagel bites, and now these healthy breakfast muffins – I now have so many delicious breakfast options to choose from. Over are the days where all I’d eat were boring scrambled eggs, or a bland bowl of cereal! These healthy breakfast muffins are perfectly sweet, totally satisfying, and the perfect fuel to get me through busy mornings. OH, and they’re great for meal prep too!

Why You’ll Love These Healthy Breakfast Muffins

These breakfast muffins are a game-changer for busy mornings. Made in just one bowl with wholesome ingredients, they’re moist, fluffy, and naturally sweetened. Whether you choose Greek yogurt, mashed banana, or applesauce, each variation offers a light and fluffy texture. Plus, they’re gluten-free and customizable with your favorite fruit or mix-ins!

overhead image of healthy oat breakfast muffins with a bite taken out.

What Makes These Muffins Healthy

  • Whole Grains: Oat flour and rolled oats provide fiber and energy to keep you fueled all morning long!
  • Natural Sweeteners: Maple syrup adds sweetness without refined sugars.
  • Healthy Fats: Olive oil contributes heart-healthy monounsaturated fats (& makes these seed oil-free!).
  • Protein-Rich: Greek yogurt and eggs boost the protein content, keeping you feeling full longer.

Frequently Asked Questions

Can I make these egg-free?

Yes! Substitute each egg with a flax egg (1 tablespoon ground flaxseed mixed with 3 tablespoons water) or use a store-bought egg replacer.

How do I store these healthy breakfast muffins?

Store them in an airtight container at room temperature for up to 3 days or refrigerate for up to a week. They also freeze well for up to 3 months.

What can I use instead of Greek yogurt?

You can use mashed banana or unsweetened applesauce as a 1:1 substitute for Greek yogurt. This not only changes the flavor profile but also caters to different dietary needs!

Can I use all-purpose flour?

Absolutely. While oat flour keeps them gluten-free, all-purpose flour can be used if gluten isn’t a concern.

healthy oat breakfast muffins on a white towel with blueberries.

Sam’s Recipe Tips

  • Customize Your Mix-Ins: Feel free to fold in nuts, seeds, or different fruits to suit your taste.
  • Don’t Overmix: Mix until just combined to keep the muffins tender.
  • Use an Ice Cream Scoop: For evenly sized muffins, use a scoop to portion the batter.
  • Check for Doneness: Insert a toothpick into the center; if it comes out clean, they’re ready.
two healthy breakfast muffins with chocolate chips stacked on top of each other.
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Healthy Oat Breakfast Muffins (3 ways!)

These healthy oat breakfast muffins are easy to make, gluten-free, and perfect for busy mornings! Made in one bowl with simple, wholesome ingredients, they come together in just minutes and are packed with flavor. Try all three variations for a nutritious, customizable breakfast the whole family will LOVE!
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Prep Time: 5 minutes
Cook Time: 20 minutes
Total Time: 25 minutes
Servings: 12 muffins

Equipment

  • 1 large bowl
  • 1 muffin pan

Ingredients

  • 1 cup Greek yogurt or 1 cup mashed banana, or 1 cup applesauce
  • 1/2 cup milk
  • 1/4 cup olive oil
  • 1/4 cup maple syrup
  • 2 large eggs
  • 1 teaspoon vanilla extract
  • 1 1/2 cups oat flour
  • 1 cup rolled oats
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1 cup fresh or frozen fruit I used blueberries, strawberries, and chocolate chips

Instructions

  • Preheat oven to 375° Fahrenheit and line a muffin tin with muffin liners.
  • In a large bowl, mix together the Greek yogurt, milk, olive oil, maple syrup, eggs, and vanilla extract.
  • Add in the oat flour, rolled oats, baking powder, and baking soda and mix until fully combined and the batter is smooth.
  • Fold in any fruit or chocolate chips you're using until it’s evenly distributed throughout the batter.
  • Then, scoop ¼ cup of batter into each muffin liner and bake muffins for 20-25 minutes, or until a toothpick inserted down the center of a muffin comes out clean. Remove the muffins from the oven and let them cool before serving or storing.

Nutrition

Serving: 1serving | Calories: 180kcal | Carbohydrates: 20g | Protein: 6g | Fat: 9g | Fiber: 3g | Sugar: 6g

Perfect carrot cake muffins, made healthy! Gluten-free, dairy-free, and refined sugar-free, yet oh-SO delicious. These healthy carrot cake muffins come together in just one bowl, in about 30 minutes!

What You’ll Need to Make Healthy Carrot Cake Muffins

Oat Flour – You can either buy pre-ground oat flour, or simply grind oats into a flour yourself. I always make my oat flour myself because it’s cheaper, and super easy. To do this, place rolled oats into a blender and blend until a flour forms, and no large oats pieces remain.

Apple Sauce – If you don’t have any apple sauce, feel free to use 1/2 cup of mashed banana instead! Though if you do use apple sauce, please make sure it’s unflavored and unsweetened for this recipe.

Maple Syrup – These refined sugar-free carrot cake muffins are naturally sweetened with maple syrup. I love the flavor of maple syrup in these muffins, you won’t even miss the sugar. However, if you don’t have any maple syrup, you can use an equal amount of honey instead!

healthy carrot cake muffins with cream cheese icing on top and milk on the side.

Tips and Tricks

  • Avoid over-mixing the muffin batter! If you mix too much, your muffins will turn out tough, instead of soft and tender. Therefore, mix all ingredients until just combined, then stop.
  • Let these healthy carrot cake muffins cool completely before icing. I know it’s tempting to ice and eat these delicious little muffins right away. But if they’re too hot when iced, the icing will melt and slide right off. So practice some self-control, and leave them to cool for at least 20 minutes first!
  • These muffins are best stored at room temperature, in an airtight container, for up to three days. However, if you live in a warm climate (or are baking these in the summer), you may want to consider storing them in the fridge. If stored in a very warm place, the cream cheese icing may spoil.

Adjust This Recipe to Your Dietary Needs

Make it Vegan: While I haven’t tested this option myself just yet, you should be able to make these vegan carrot cake muffins by substituting the eggs for flax eggs! Or, use this Bob’s Red Mill Egg Replacer in place of the eggs in this recipe.

Healthy Carrot Cake Muffins with Cream Cheese Icing

5 from 2 votes
Recipe by Samantha Course: Snacks, DessertDifficulty: Medium
Servings

12

muffins
Prep time

10

minutes
Cooking time

20

minutes
Total time

30

minutes

Perfect carrot cake muffins, made healthy! Gluten-free, dairy-free, and refined sugar-free, yet oh-SO delicious. These healthy carrot cake muffins come together in just one bowl, in about 30 minutes!

Ingredients

  • 2 eggs

  • 1/2 cup apple sauce, unsweetened

  • 1/2 cup maple syrup

  • 1/4 cup milk, I used non-dairy milk

  • 1 teaspoon vanilla extract

  • 2 cups oat flour

  • 1 teaspoon cinnamon

  • 1 teaspoon baking powder

  • 1/2 teaspoon baking soda

  • 1/4 teaspoon nutmeg

  • 1/4 teaspoon salt

  • 1 cup shredded carrots

  • 1/4 cup chopped walnuts or pecans

  • 1/4 cup raisins

  • For the cream cheese icing:
  • 1/4 cup softened cream cheese, I used non-dairy cream cheese

  • 3 tablespoons softened butter, I used non-dairy butter

  • 2 cups powdered sugar

  • 2-3 tablespoons milk, I used non-dairy milk

  • 1/4 teaspoon vanilla extract

Directions

  • Preheat oven to 350° Fahrenheit and line a muffin tin with muffin liners.
  • In a large bowl, mix together the eggs, apple sauce, maple syrup, milk, and vanilla extract.
  • Add in the oat flour, cinnamon, baking powder, baking soda, nutmeg, and salt. Mix until everything is just combined.
  • Then, fold in the shredded carrots, chopped walnuts, and raisins until evenly distributed throughout the batter.
  • Bake muffins for 20-25 minutes, or until a toothpick inserted down the center of one muffin comes out clean. Remove muffins from oven and transfer to a wire cooling rack to cool completely.
  • While muffins cool, make the cream cheese icing by adding all ingredients to a bowl and whisking until smooth and well-combined. Then, spread or pipe cream cheese icing on top of each cooled muffin.

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Perfectly fluffy and delicious coffee cake muffins made gluten-free, with a dairy-free option as well! They’re irresistibly soft, sweet, and complete with a cinnamon streusel topping. I especially love enjoying a warm gluten-free muffin with my coffee in the morning – there’s no better way to start the day!

three gluten-free coffee cake muffins stacked on top of each other

What You’ll Need For This Recipe

Gluten-Free All Purpose Baking Flour – I use Bob’s Red Mill Gluten Free 1-1 Baking Flour in most of my gluten-free baking recipes. It bakes up beautifully and can pretty much be used as a 1:1 swap for regular all purpose flour! However, you can use any gluten-free all purpose baking flour you’d like. Though when it comes to gluten-free flours, it’s super important to the integrity of your bake that your flour contains xanthan gum. Xanthan gum creates structure and will essentially hold these muffins together. Therefore, if your gluten-free flour doesn’t have xanthan gum, supplement it with 1 teaspoon of xanthan gum in this gluten-free coffee cake muffins recipe.

Butter – Any butter you’d like will work here! Salted, unsalted, and non-dairy butter all bake perfectly in this recipe. When it comes to salted butter, I truly don’t believe any butter has enough salt in it to make any difference in a recipe. So, feel free to use whatever butter you have on hand!

Eggs – Bring your eggs to room temperature before getting started on this delicious breakfast or snack recipe. By doing this, we reduce the risk of the cold eggs re-solidifying the melted butter. It’s also always a great rule-of-thumb to have all ingredients at room temperature before starting on any baked goods recipe!

Top Tips

  • You can freeze leftover gluten-free muffins for up to 3 months! I currently have half my batch in the freezer right now, ensuring they don’t go bad before I have a chance to eat them. Though for muffins you plan on eating right away, simple store them in an airtight container at room temperature for up to 1 week.
  • Avoid over-mixing the batter, as this could result in tough and chewy muffins! Therefore, when folding the wet ingredients into the dry, simply mix until no more flour pockets remain. Once just combined, put down the spatula and head straight into the next step!
  • These muffins are best enjoyed warm! So to warm them up after baking, I recommend either popping them in the microwave for 10-15 seconds, or into the toaster for a couple of minutes. Once warm, they’re irresistibly soft and flufy!

Adjust This Recipe To Your Dietary Needs

Make it Vegan – While I haven’t tried this variation myself yet, you may be able to get away with replacing the eggs in these muffins with a vegan egg substitute. I’ve used the Bob’s Red Mill Vegan Egg Substitute in other recipes, and have almost always found it successful. Flax eggs might work here as well, though expect a slightly more dense gluten-free muffin if going that route.

Cut the Recipe in Half – This recipe makes 24 gluten-free coffee cake muffins, but if that sounds like too much for you, you can easily cut this recipe in half! That’s right, use half of all ingredients listed for just 12 perfect muffins.

Use Regular Flour – Feel free to simply swap the gluten free all purpose flour for regular all purpose flour in this recipe.

Other Delicious Mix-Ins

Instead of the cinnamon and streusel topping, feel free to add one of the following to your gluten-free muffins:

  • Blueberries
  • Sliced Bananas
  • Chocolate Chips
  • Cranberries and Orange Zest
  • Lemon Juice and Poppyseeds
  • Strawberries
  • Raspberries
  • or simply leave them plain!

Perfect Gluten-Free Coffee Cake Muffins

3 from 112 votes
Recipe by Samantha Course: BreakfastDifficulty: Easy
Servings

24

servings
Prep time

10

minutes
Cooking time

20

minutes
Total time

30

minutes

Perfectly fluffy and delicious coffee cake muffins made gluten-free, with a dairy-free option as well! They’re irresistibly soft, fluffy, sweet, and complete with a cinnamon streusel topping. I especially love enjoying a warm gluten-free muffin with my coffee in the morning – there’s no better way to start the day!

Ingredients

  • For the gluten-free muffins:
  • 3 cups gluten-free all purpose baking flour

  • 2 teaspoons baking powder

  • 1 teaspoon cinnamon

  • 1/2 teaspoon salt

  • 1 cup sugar

  • 1 cup butter, melted (I used non-dairy butter)

  • 3/4 cup milk (I used non-dairy almond milk)

  • 3 eggs, at room temperature

  • 1 teaspoon vanilla extract

  • For the crumb topping:
  • 1 cup gluten-free all purpose baking flour

  • 1 cup brown sugar

  • 1/2 cup butter, softened

  • 1 teaspoon cinnamon

Directions

  • Preheat oven to 350° Fahrenheit and line a muffin tin with cupcake liners.
  • Mix together the flour, baking powder, cinnamon, and salt in a large bowl.
  • In a separate bowl, whisk together the sugar, melted butter, milk, eggs, and vanilla extract.
  • Slowly pour the wet ingredients into the dry ingredients, mix until just combined. Fill each muffin mold with about ¼ cup of batter.
  • Mix together all crumb topping ingredients in a bowl, then sprinkle over each muffin.
  • Bake for 20-25 minutes or until a toothpick inserted down the center of a muffin comes out clean. Let cool in tin for 10 minutes before transferring to a wire cooling rack to cool completely.

Notes

  • Gluten-Free All Purpose Flour: I used Bob’s Red Mill Gluten Free 1:1 Baking Flour.
  • Butter: I used Earth Balance Vegan Buttery Sticks to make this recipe dairy-free.

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