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Healthy Breakfast Muffins

These Healthy Breakfast Muffins are perfect for busy mornings. Packed with fibre, protein and the goodness of fruit AND veggies, these muffins are a great way to start the day. These apple, banana and carrot muffins are freezer friendly so they are great to prep in bulk….not to mention they taste amazing! 

What’s on the menu for breakfast at your house? I must admit, especially during the week my kids go for toast and cereal. But I am trying to change that! I would love my kids to get more nutrition into their morning meals – and ideally some veggies. Is that too much to ask? 

But it’s not practical for me to cook breakfasts during the week. Mornings are chaotic enough without adding that to the mix.

Enter these Healthy Breakfast Muffins! My Blueberry Bran Muffin recipe have been an absolute hit with my eldest kid, so I wanted to develop another bran based breakfast muffin…and pack even more goodness into them!

And this muffin recipe has really hit the mark. They are absolutely packed with fibre and protein. Not to mention loaded with fruit and veggies. So they are great for kids and adults alike for a nourishing start to the day. 

image of healthy breakfast muffins in a dish

This breakfast muffin recipe is made with apple, bananas and carrots along with wholemeal flour and bran so they’re a great source of fibre.

But not only are they full of goodness – they taste great too! A deliciously sweet muffin that is not loaded with refined and added sugar (and you can even reduce the amount if you’d like) They have a lovely soft texture with a great crumb. And the cinnamon adds a comforting and warming flavour.

Healthy Breakfast Muffins

Ingredients and Substitutions

These Healthy Breakfast Muffins use easily sourced ingredients – you probably have most if not all already in your pantry and refrigerator! 

  • Overripe Banana – the riper the banana the sweeter it will be. I like to use bananas that have a deep yellow colour with brown spots. I like to mash the banana with a fork on a clean chopping board – so much easier than mashing in a bowl!
  • Greek Yogurt – adds extra protein to the recipe and helps keep the muffins nice and moist. You can substitute with ricotta, cottage cheese or sour cream. You could also use a natural yogurt. I use an un-sweetened Greek Yogurt. 
  • Eggs – eggs help bind and leaven the recipe and also add protein. 
  • Low Flavoured Olive Oil – you can use avocado oil or any other baking oils
  • Milk – adds moisture to the recipe. I have tested this breakfast muffin recipe without the milk but the texture is far superior with this ingredient. 
  • Brown Sugar –  you can reduce the amount of sugar in this recipe if you like or substitute with white sugar. I just prefer brown sugar as it makes a softer bake. You could also substitute with maple syrup.
  • Vanilla Extract – adds flavour and brings out the sweetness of the ingredients. You could use vanilla bean paste or essence if this is what you have on hand.
  • Cinnamonoptional but adds a lovely flavour to the recipe so I would recommend using it! 
  • Carrot – a great source of vitamins and minerals, especially beta carotene. They are a good source of fibre. 
  • Apple – adds a sweetness to the recipe and is a great source of vitamin c and fibre. You do not need to remove the liquid from the apples after grating.
  • Wholemeal Flour – also known as whole wheat flour. You can use a refined flour if you like. I have not tested with gluten free variations. 
  • Wheat Bran – you can normally get this ingredient in the cereal section in the supermarket. This adds a slightly nutty taste to the muffin and adds extra fibre to these Breakfast Muffins. 
  • Baking Powder – a leavening ingredient. 
  • Baking Soda – a leaving ingredient. I like the taste that baking soda adds to these muffins but if you do not have it replace with the same amount of baking powder.

How to make Healthy Breakfast Muffins

Preheat your oven to 180c fan bake and line and grease a medium muffin tray. In a large bowl add in the banana, greek yogurt, eggs, olive oil, milk, brown sugar, cinnamon and whisk together until well combined. Then add in the apple and carrot and stir until evenly mixed through.

collage of Breakfast Muffins being mixed

Then add in the wholemeal flour, wheat bran, baking powder and baking soda. Stir the ingredients through until just combined. Do not over-mix. 

bowl of muffin mixture. the dry ingredients have been added to the banana carrot and apple mixture

Once mixed until just combined, evenly spoon into the muffin tray and bake for around 15 minutes or until a skewer inserted into the centre of the muffin comes out clean and the top of the muffin bounces back when pressed gently. 

picture of a cooked Health Breakfast Muffin in a muffin tray

Can I freeze muffins? 

One of the great things about muffins is that they are great to prep ahead and freeze for later. Once you have baked the muffins, cool completely then add into a ziplock bag or container and freeze for two-three months. The defrost well either at room temperature, in the fridge or using the defrost setting in your microwave. 

close up image of muffins in a bowl

Love these Healthy Breakfast Muffins? You may also love these recipes:

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Healthy Breakfast Muffins

Healthy Breakfast Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 2 reviews
  • Author: Bernadette - Goodie Goodie Lunchbox
  • Prep Time: 10 minutes
  • Cook Time: 15 minutes
  • Total Time: 25 minutes
  • Yield: 18 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: Western


Packed with fibre, protein and the goodness of fruit AND veggies, these Healthy Breakfast Muffins are a great way to start the day. They are freezer friendly so they are great to prep in bulk for those busy school mornings.


  • 150g (one medium) mashed overripe banana
  • 1 cup (205g) un-sweetened Greek Yogurt
  • 2 eggs
  • 1/2 cup (125ml) low flavoured olive oil
  • 1/2 cup (125ml) milk
  • 1/2 cup (100g) brown sugar (you can reduce to 1/3 cup for a lower sugar option)
  • 1 teaspoon vanilla extract
  • 1 teaspoon ground cinnamon
  • 1 medium (110g) apple grated
  • 1 medium (55g) carrot grated
  • 1 1/2 cup (205g) wholemeal (whole wheat) flour (plain, unleavened)
  • 1 1/4 cups wheat bran
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda


  1. Preheat your oven to 180c fan bake and line and grease a medium muffin tray.
  2. In a large bowl mix together the mashed banana, greek yogurt, olive oil, milk, eggs, brown sugar, vanilla and cinnamon until well combined.
  3. Stir through the grated apple and carrot until evenly mixed.
  4. Add in the flour, wheat bran, baking powder and baking soda and mix gently until just combined.
  5. Spoon into the prepared muffin tin and bake for around 15-18 minutes or until a skewer inserted into the centre of a muffin comes out clean and when you press the top of the muffin gently it bounces back.
  6. Remove from the oven and stand in the muffin tin for 5 minutes before cooling on a wire baking rack. If storing for later cool completely then freeze in a zip lock bag.

I hope you and your family enjoy this Healthy Breakfast Muffin recipe! I would love you to share pictures of your family making and enjoying these so be sure to share with me over on Facebook or Instagram. If you have some time, I would love for you to rate this recipe! 

Happy baking, 

Bernadette x

Healthy Breakfast Muffins


  1. Could you just use self raising white flour if there is no whole meal? It’s out of stock everywhere!

  2. These are absolutely delicious and so easy to make. I didn’t have wheat bran on hand so used oat bran, and still turned out perfect. My son ate 3 in one sitting! Thanks for another great recipe!

  3. Delicious! The whole family loved them. Will be making these again

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