These gluten free apple muffins are made using a combination of buckwheat (or all-purpose gf) and almond flours, a generous amount of apple and a moderate amount of sugar. They are easy to make, fluffy, moist and delicious, perfect for a quick breakfast or as a snack.
See also gluten free blueberry muffins and rice with apples!

These gluten free apple muffins are made with lots of juicy apples so they are moist, fruity and delicious. They are also moderately sweet, high in fibre and easy to make. They come with a crunchy topping of maple coated flaked almonds for a delicious autumnal breakfast or snack.
I made these healthy apple muffins using a combination of naturally gluten free buckwheat four (also delicious in crepes) as well as almond flour. Buckwheat flour has a distinctive, nutty, slightly malty flavour, which in some recipes can be a little overpowering when used alone. The almond flour mellows the buckwheat flavour and improves the texture of the muffins.
If you prefer to use all-purpose gluten free flour (instead of buckwheat) please read my tips below.
Gluten free apple muffins - ingredients and substitutions

- Apples: I like to use sweet tasting apples in this recipe, but you can use a tart variety. If your apples are quite sour add an extra tablespoon of sugar.
- Buckwheat flour: or all-purpose/plain gluten free flour (see details below).
- Almond flour/ground almonds: tones down the buckwheat and produces a fluffy texture.
- Baking powder: ensure it's gluten free (if required).
- Bicarbonate of soda.
- Light brown sugar: adds a hint of caramel and helps keep these muffins moist. You can use coconut, cane or muscovado sugar, instead.
- Eggs.
- Yogurt: improves the texture.
- Milk: use any.
- Oil: use any mild tasting oil.
- Cinnamon: I tested this recipe also with pumpkin spice, ginger and nutmeg, none of which worked as well as cinnamon alone, though you can add whichever spices you like.
- Flaked almonds and maple syrup for a sweet, crispy topping.
All-purpose gluten free flour vs buckwheat flour
I tested these gf apple muffins using both buckwheat as well as all-purpose (plain) gluten free flours (in combination with almond flour). While both produced fluffy muffins I found the all-purpose flour slightly more grainy. The buckwheat version also had better structure, which is why I prefer to use buckwheat.
However, if you'd rather use all-purpose gluten free flour add an extra tablespoon. This flour tends to be a blend of rice, corn, potato, tapioca and sometimes buckwheat flours (which all have different weights), and if you measure your ingredients using a scale you will need 155g (which is about a cup) plus one tablespoon.
For best results I recommend that you always combine these flours with almond flour.
How to prepare the apples
I used coarsely grated apples to ensure the fruit is distributed evenly throughout the batter. This can be done quickly using a box grater - you only have to peel the apples (the core can be easily avoided as you grate).
Another advantage of grating the apples is to ensure these gluten free apple muffins are moist throughout. Cubed apples, typically used in apple muffins, don't work as well in the gluten free version and I strongly recommend grating the apples, instead.
Step-by-step recipe instructions
1. Preheat the oven to 400F/200C/180 fan/gas mark 6. Lightly grease a 12-hole muffin pan or line with paper cases and set aside.
2. Prepare dry mixture: Combine the flours, baking powder, bicarbonate of soda and cinnamon. Stir thoroughly using a whisk.


3. Prepare wet mixture: Whisk together the eggs, oil, yogurt, milk and sugar until smooth and creamy.


4. Prepare and add apples: Peel and coarsely grate the apples (discarding the core) then stir into the egg mixture.

5. Assemble: Add the dry mixture into the wet ingredients and stir only until the dry ingredients are no longer visible. The batter will be quite thick.

6. Bake: Divide the batter between 12 muffin cases. In a bowl mix together the flaked almonds with the maple syrup and place a small amount on top of each muffin (this is optional). Bake in the centre of the oven for 23 minutes. If your muffins start to brown too much lower the heat to 375F/190C/gas 5 after about 18 minutes (not sooner).

7. Cool: Remove from the oven and set aside for 15-20 minutes then transfer to a rack to cool completely.

Serving suggestions
These moist gluten-free apple muffins are delicious for breakfast either on their own or with cream cheese/cottage cheese for a more substantial meal. You can also enjoy them with a thin layer of peanut butter or another nut butter. They make a fantastic wholegrain snack, perfect to enjoy throughout the fall.
Can I use different fruit
Yes, you can use pears (make sure they are firm so you are able to grate them). You can also use a combination of apples and pears. Another option is to add a little grated carrot into the mix (but remember to stick to the recommended weight).
Top tips
- Peel and grate the apples just before adding into the batter (apples are prone to discoloration).
- I prefer sweet tasting rather than tart apples in these muffins, but you can use any (if your apples are quite tart add an extra tablespoon of sugar).
- Do not overmix the batter. Stir just to combine.
- Delicious with maple flavoured flaked almonds on top, though this step is optional.
- These gluten free muffins with grated apple are best served cooled completely. Keep them covered with a kitchen towel and place in a container the following day. After that keep them refrigerated for 2 more days. They will stay moist and fresh for up to 4 days!
- Freeze for up to 3 months.
Related recipes to try next
- Cherry Crumble (Gluten Free)
- Stuffed Baked Apples with Pecans (Gluten Free)
- Quinoa Egg Muffins (Gluten Free)
- Autumn Pear Muffins (Low Sugar)
See also these other easy, delicious breakfast recipes!
Recipe

Gluten Free Apple Muffins (Low Sugar)
Equipment
- Box grater
- 12-hole muffin pan
Ingredients
- 12.35 ounces (350 g) apples approx. 3 medium apples
- 1 cup (135 g) buckwheat flour *see Notes for alternative
- 1¼ cups (115 g) almond flour
- 2 teaspoons baking powder ensure it's gluten free if required
- ½ teaspoon bicarbonate of soda
- 2½ teaspoons cinnamon
- 2 large eggs at room temperature
- ⅔ cup (160 g) yogurt at room temperature
- 1 tablespoon milk at room temperature
- ⅓ cup+1tbsp (80 g) light brown sugar
- ⅓ cup+2tsp (90 ml) oil any
- 5 tablespoons flaked almonds optional
- 2 teaspoons maple syrup optional
Instructions
- Preheat the oven to 400F/200C/180 fan/gas mark 6. Lightly grease a 12-hole muffin pan or line with paper cases and set aside.
- Prepare dry mixture: Combine the flours, baking powder, bicarbonate of soda and cinnamon. Stir thoroughly using a whisk.
- Prepare wet mixture: Whisk together the eggs, oil, yogurt, milk and sugar until smooth and creamy.
- Prepare and add apples: Peel and coarsely grate the apples (discarding the core) then stir into the egg mixture.
- Assemble: Add the dry mixture into the wet ingredients and stir only until the dry ingredients are no longer visible. The batter will be quite thick.
- Bake: Divide the batter between 12 muffin cases. In a bowl mix together the flaked almonds with the maple syrup and place a small amount on top of each muffin (this is optional). Bake in the centre of the oven for 23 minutes. If your muffins start to brown too much lower the heat to 375F/190C/gas 5 after about 18 minutes (not sooner).
- Cool: Remove from the oven and set aside for 15-20 minutes then transfer to a rack to cool completely.
Notes
- *You can use all-purpose/plain gluten free flour, instead, but add an extra tablespoon. If your gf flour blend contains rice, corn, potato and/or buckwheat flours (or similar) use 155g (equivalent of 1 cup) plus one tablespoon.
- Peel and grate the apples just before adding into the batter (apples are prone to discoloration).
- I prefer sweet tasting rather than tart apples in these muffins, but you can use any (if your apples are quite tart add an extra tablespoon of sugar).
- Do not overmix the batter. Stir just to combine.
- Delicious with maple flavoured flaked almonds on top, though this step is optional.
- These gluten free muffins with grated apple are best served cooled completely. Keep them covered with a kitchen towel and place in a container the following day. After that keep them refrigerated for 2 more days. They will stay moist and fresh for up to 4 days!
- Freeze for up to 3 months.
Nutrition
*Nutritional information is automatically generated and should be considered as an estimate.
**A note about baking: If using a fan-assisted oven refer to your appliance's instructions and adjust the temperature accordingly.
Keep in touch!
If you make this gluten-free apple muffin recipe I'd love to know how it turned out for you. Did you make any substitutions? Let me know in the comments below, thanks!
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Tristyn says
Where do you find your buckwheat flour? Any one I’ve bought ends to being brown and super dry with baking
Monika says
This always depends on the recipe. I don't buy the same brand of buckwheat flour but in my experience they are all the same. These muffins are quite moist thanks to the apples. If you make them let me know how they turn out!
JC says
These look delicious! I'd like to try this recipe. Are " almond flakes" the same as "ground almonds?" I'm not clear what almond flakes are and if they get sprinkled on top of the muffins before baking? Thank you!
Monika says
Almond flakes are thinly sliced almonds, and yes, you sprinkle them on top of the muffins before baking (see photos). Hope this helps:)
Kate says
Hi, Monica. Thanks for sharing this recipe. I am looking forward for my daughter. But I want ask can I replace almond flour to coconut flour? Would it be okay? Thanks 😊 Kate from Cambridge uk.
Monika says
Hi Kate, I wouldn't recommend it, unfortunately. Coconut flour absorbs moisture differently than almond flour so the amount wouldn't be the same, but I can't tell you what it is without testing it first. I am guessing it would be less.
Cindy says
Made these for bible study group. Was a hit! Several of us are gluten free and refined sugar free. I exchanged apple sauce for the oil, added 1/8 tsp ground cloves, and a little zested nutmeg. I'll definitely make these again! Maybe adding a little more spice. Like an apple spice muffin. Thanks for the recipe!
Monika says
I like your tweaks! Thank you for your feedback:)
Sally says
I used fruit purée. 200g. Also one whole egg with 2 egg whites. Delish
Monika says
Fantastic, thanks for the feedback:)
Elizabeth says
I have made these muffins now multiple times with either apples or pears and, more recently, half apple and half rubarb (I did add 20 gr of suger to make up for the tartness of the rubarb). This recipe is seriously no fail!
Monika says
That's fantastic! Thanks for the feedback:)
Michelle says
Perfect recipe. Just the right amount of sweetness (I find most recipes overly sweet) and cooked perfectly. I squeezed out some of the juice from the apples before adding them.
Monika says
Glad you enjoyed these! I understand why you would want to get rid of some of the juice from the apples but you don't need to worry about too much moisture if you add the apples into the batter as soon as you've grated them. Really appreciate the feedback:)
Elizabeth says
I made these muffins this morning and they are absolutely, hands down, the best GF muffins I have ever made! They are moist and the sweetness is perfect (IMO). The only change I made was using almond milk (so for you dairy-free folks: that works too!) I love baking by weight as I find the results are typically better. I would definitely recommend weighing your grated apples as I found that 2 were just enough. Thanks so much for this recipe! I will be trying this with pears too for sure 🙂
Monika says
Glad you liked these muffins! I totally agree that weighing ingredients produces better results in baking. Thanks so much for the feedback:)
Monika says
Thank you! They are much healthier indeed, with a lot less sugar, and they also stay moist even the next day:)