As a nutritionist and a sweet tooth, I wanted to create a recipe that satisfied the sweet craving while delivering on nutrients like protein, fibre, healthy fats and complex carbohydrates. These healthy muffins tick all of these boxes, helping to stabilise blood sugar levels and keep hunger at bay, all while being quick and easy to make. Some bonus nutrients in this recipe are calcium and B vitamins! If you love a good chocolate chip muffin but want something that’s actually going to nourish you, these High Protein Chocolate Chip Muffins are the answer.
Everything you need to make Gluten Free Protein Choc Chip Muffins
You only need 11 ingredients to make these muffins and most of them are pantry staples if you bake gluten free regularly. Everything you need is listed below along with ingredient notes and possible substitutions. As usual, all of the ingredient quantities are in the recipe card at the bottom of this post.
Wet Ingredients
- large eggs – eggs provide structure and moisture to the muffins and are a great source of protein and essential nutrients including B12 and choline.
- soy milk – I’ve used soy milk here to add extra protein as it has a higher protein content than most other plant milks. You could also use whole milk, oat milk or any milk of your choice.
- extra virgin olive oil – olive oil keeps these muffins beautifully moist and adds heart-healthy monounsaturated fats. It’s my go-to oil for cooking and I would use it over canola oil any day! You won’t taste the olive oil at all once baked, it creates a really lovely, tender crumb.
- pure maple syrup – maple syrup is the only sweetener in this recipe, keeping these muffins refined sugar free. It adds a lovely caramel-like sweetness that pairs perfectly with the chocolate and vanilla. Make sure to use pure maple syrup, not maple-flavoured syrup.
- vanilla extract – Use a good quality pure vanilla extract for the best flavour.
Dry ingredients
- almond flour – almond flour is the base of these muffins and is what keeps them so moist and tender. It’s naturally gluten free and adds protein, healthy fats, vitamin E and fibre. Make sure to use finely ground almond flour rather than more coarsely ground almonds (almond meal) for the best texture.
- tapioca flour – tapioca flour helps to lighten the texture and also helps bind everything together. You may also see this labelled as tapioca starch, they’re the same thing.
- buckwheat flour – despite the name, buckwheat is completely gluten free! It adds a lovely earthy, slightly nutty flavour and is rich in fibre, magnesium and antioxidants. It’s one of my favourite gluten free flours to bake with.
- vanilla whey protein powder – I’ve used Chief Nutrition Vanilla Whey Protein Powder in this recipe, which adds a beautiful vanilla flavour and a serious protein boost. If you use a different brand, the results may vary slightly as protein powders can differ in texture and flavour. If you need these to be dairy-free, you could try a plant-based vanilla protein powder but the texture may differ. I prefer Chief Nutrition whey protein powders as they are grass fed and tested for heavy metals and other contaminants.
- baking powder – make sure your baking powder is fresh for the best rise. If yours has been open for a while, test it by adding a teaspoon to hot water, it should fizz. Also check that your baking powder is gluten free if needed and make sure you’re using baking powder and not baking soda!
- dark chocolate chips – dark chocolate chips are the star of these muffins! I used mini chocolate chips, which work really well as they don’t sink to the bottom of the muffin. If you don’t have any choc chips, you can use roughly chopped good quality dark chocolate (70% cocoa or higher).

Variations
Use the batter as a base and swap the chocolate chips for other mix-ins like berries, sultanas or white chocolate.
Equipment you will need
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Tips for the Best Chocolate Chip Protein Muffins
Here are a few tips to make sure your muffins turn out perfectly every time:
- Sieve the dry ingredients – sieving the tapioca flour, buckwheat flour and baking powder removes any lumps and aerates the flour, giving you a lighter muffin.
- Use conventional oven (not fan forced) – this recipe works best in a conventional oven. Fan forced can cause the tops to brown too quickly while the centres are still underdone. If you only have fan forced, reduce the temperature by about 20°C and keep an eye on them.
- Don’t substitute the flours 1:1 – each flour in this recipe plays a specific role (moisture, structure, lightness) so I wouldn’t recommend swapping them out. If you do need to substitute, the results may differ.
- Use paper muffin liners – line the muffin pan with liners for easier cleaning up. If you’re not using liners then make sure to grease the pan really well with butter, olive oil or avocado oil.
- Fill the liners evenly – use an ice cream scoop or large spoon to divide the muffin batter evenly between the 10 liners for consistent baking.




Storage
Once cooled to room temperature, transfer to an airtight container and store at room temperature for up to 1-2 days, or in the fridge for up to 5 days. If you are storing in the fridge, you might want to gently warm the muffins in the microwave to return the muffin to it’s just baked softness.
These muffins also freeze beautifully! Place them in a single layer in a freezer bag or airtight container and freeze for up to 3 months.
To defrost: Remove from the freezer and thaw at room temperature for 1-2 hours. Once thawed, pop in the microwave for 30-40 seconds for a warm, freshly-baked taste. They’re honestly so good straight from the freezer and microwaved, the chocolate chips go all melty again!

High Protein Chocolate Chip Muffins

Equipment
- Whisk
- Muffin pan
- Muffin liners
Ingredients
- 2 eggs
- 1/3 cup soy milk
- 1/3 cup extra virgin olive oil
- ½ cup pure maple syrup
- 2 teaspoons vanilla extract
- 1 ½ cups almond flour
- ½ cup tapioca flour
- ½ cup buckwheat flour
- ½ cup Chief Vanilla Whey Protein Powder
- 1 ½ teaspoons baking powder
- ¾ cups dark chocolate chips
Instructions
- Preheat the oven to 180°C/356°F (conventional). Line a muffin tray with 10 muffin liners and set aside.
- Add the eggs, milk, olive oil, maple syrup and vanilla extract to a bowl and whisk to combine.
- Add the almond flour to the bowl and sieve in the tapioca flour, buckwheat flour, Chief Vanilla Whey Protein Powder and baking powder. Stir until well combined. Add the choc chips to the bowl and stir until just combined.
- Divide the mixture between the muffin liners and place into the oven to bake for 22 minutes or until golden brown and cooked through when tested with a skewer.
- Once baked, remove from the oven and set aside to cool. Once cooled to room temperature, transfer to an airtight container.



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