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Healthy Blueberry Muffins Recipe – Step by Step

Blueberry muffins recipe made healthy with no refined sugar added. Since LilS was born, I have been more mindful of use of refined sugar and flour in my baked goods.

healthy blueberry muffins recipe

I have been trying and loving recipes from Cookie and Kate recently and this healthy blueberry muffin recipe is adapted from hers too. So what makes these muffins healthy? Or rather, healthier?

  • They are refined sugar free
  • They use whole wheat flour (like atta or spelt flour)
  • Blueberries add a lovely colour and tang naturally
  • You can adjust sweetness levels without compromising flavour or texture
  • They are a great way to get some yogurt into your child, especially if they don’t like to eat it plain

I have used atta (Indian whole wheat flour) and spelt flour with equal success. You can also use a mix of all purpose flour and a healthier flour if you are worried about texture or a beginner baker. You may also like these blueberry streusel muffins or these banana oats atta muffins which are also great for toddlers.

May I also recommend this AMAZING mini muffin pan that I am now using? It needs no greasing and the muffins pop out of it so smoothly when baked. I am in love and have used it numerous times already. Well worth the price and clean up is super quick too. *Fan Girl*



Healthy blueberry muffins recipe using no refined flour or sugar. Perfect to make as a toddler snack.


  • 1 and 3/4 cup atta or spelt flour
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • A pinch of salt
  • 1/3 cup extra virgin olive oil (I have used regular olive oil and veg oil with success)
  • 1/3 cup honey (can be increased to 1/2 cup)
  • 2 eggs
  • 1 cup plain yogurt (Greek yogurt works better)
  • 1 tsp vanilla extract
  • 1 cup blueberries (fresh or frozen)


  1. Pre-heat oven to 350 F / 180 C. Line or grease your muffin pan as needed. I used my mini muffin pan
  2. In a bowl, combine the flour with the baking powder, baking soda and salt. Mix them together with a whisk until well combined. You can also sift this mixture but who has time for things like that anymore? Not me!
  3. In a separate bowl, add the oil and honey and beat together with a whisk.
  4. Add the eggs and beat well, then add the yogurt and vanilla. Mix everything well together
  5. Gently pour the wet ingredients into the dry ingredients and fold with a silicon spatula or wide spoon. Do not be tempted to over mix at this stage, just combine everything as gently as you can
  6. The batter is a bit tick so I use a spoon to pour into the muffin pan. 
  7. At the end, add 1-2 blueberries per muffin and gently press into the top. I prefer doing this to adding the blueberries to the batter because that makes them sink to the bottom and become gooey on baking
  8. Bake in the pre-heated oven for 20 minutes. Start checking from around 17 minutes and bake until the top turns golden brown and a skewer inserted into the muffin comes out with wet crumbs
  9. Cool in the muffin pan for 10 minutes and gently invert onto a baking tray and cool completely


  • If you make normal sized muffins, you will get around 12 of them. In that case, add 4-5 blueberries per each muffin
  • This yields a mildly sweet muffin. Increase amount of honey if you want it a tad sweeter. You can also add some sugar on top of the warm muffins as soon as they come out of the oven, for a crispy outer layer
  • You can add some cinnamon powder for extra flavour and health kick

Keywords: healthy blueberry muffin, toddler friendly snacks, muffins for toddlers

Step by Step Pictures for Making Healthy Blueberry Muffins

1. Mix together the flour, baking powder, baking soda, salt, and cinnamon (if using)
healthy blueberry muffins recipe
2. In a separate bowl, whisk together honey, oil, and eggs
healthy blueberry muffins recipe
3. Add yogurt to this and whisk again until well combined
healthy blueberry muffins recipe
4. The wet ingredients should be smooth but a few small lumps from the yogurt is fine
healthy blueberry muffins recipe
5. Pour wet ingredients into the dry ingredients
healthy blueberry muffins recipe
6. Fold GENTLY with a spatula until just combined. Do not over mix the batter
healthy blueberry muffins recipe
7. Spoon into the muffin pan
healthy blueberry muffins recipe
8. Press 1-2 blueberries into each muffin
healthy blueberry muffins recipe
9. Bake in a pre-heated oven for 17-22 minutes. Mine usually get done in 20 minutes or so. If using a regular muffin pan, it will take longer
healthy blueberry muffins recipe
10. The muffins are done when the top is golden brown and a skewer inserted to them comes out clean or with moist crumbs
healthy blueberry muffins recipe
Easily the most moist and delicious healthy blueberry muffins I’ve tried!


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