You only need 5 minutes prep to make these keto apple muffins! This easy recipe contains real apple and no fake extracts, yet the net carb count is really low. A family favorite.

We love these low carb apple muffins for breakfast or as a snack. They are gluten free, gently sweet, packed with flavor and studded with juicy apple pieces. Yum, and all that at only 5.2g net carbs per muffin!
I've also added flaxseed to the muffin batter, which increases the fibre content. This recipe is filling, yet light.
The muffins taste (and smell) divine when they are warm. Of course, they are just as delicious cold. I pack them into lunchboxes or grab one when I need a quick treat on the go.
I also love this Keto Apple Cake.
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Ingredients
Here are the ingredients you need for sugar free apple muffins:

- Apples - Any dessert apple works well, from Braeburn to Golden Delicious to Granny Smith. Peel, core and chop them.
- Almond flour and coconut flour - I love using these flours in combination, it makes keto muffins taste so good.
- Ground flax - Adds fibre and a better crumb structure.
- Sweetener - I used granulated Bocha Sweet. Any erythritol monk fruit blend will also work well, white or golden. As would allulose or xylitol.
- Eggs - Large and room temperature for a better rise.
- Cinnamon, vanilla extract and baking powder - The spices are essential, they really lift the apple taste.
- Apple cider vinegar - My secret ingredient. Increases the apple flavor and makes the crumb super fluffy and light. Cannot be replaced with any other vinegar!
- Cream cheese - You could use sour cream instead or a mix of yoghurt and butter.
See the recipe card for full information on ingredients and quantities.
Instructions
Let me show you how to make Keto Apple Muffins, step by step. It's easy!
Scroll down to the recipe card for the detailed method with timings and nutrition info.

MACERATE APPLES
Put the chopped apples in a bowl with lemon juice and sweetener and let them sit.

BLEND WET INGREDIENTS
Blend the eggs and sweetener until frothy. Add the cream cheese, apple cider vinegar and vanilla extract. Mix until smooth.

ADD DRY INGREDIENTS
Stir together the dry ingredients in a separate bowl. Then add them to the egg mixture and blend until a smooth batter forms.

FOLD IN APPLES
Drain excess liquid from the bowl with the chopped apples. Fold the apples into the muffin batter.

FILL MUFFIN CUPS & BAKE
Fill the batter into a muffin pan lined with paper cups. Sprinkle with sweetener and cinnamon.
Bake in the preheated oven until the tops lightly browned and a skewer inserted comes out clean.
Katrin's Top Tips
#1 Want fluffy muffins? Macerate the apples. This process draws out the liquid in the fruit (It was 2 tablespoons for me). It prevents the muffins from being soggy.
#2 Patience. The batter is quite liquid at first, but firms up as the flax and coconut flour soak up the moisture.
#3 Don't overfill. Leave a little space at the top of the muffin cups. The batter will rise and you don't want it to spill over.
#4 Enjoy warm or cold. Apple muffins taste wonderful when they are still warm. Just know that they will be a little fragile straight out of the oven. They firm up as they cool.
Variations
For a richer muffin - Replace half of the cream cheese with butter for a more cake-like experience.
Use apple pie spice - Make them taste like apple pie by adding ½ teaspoon nutmeg and ¼ teaspoon each allspice, ginger and cardamom.
Keto applesauce muffins - Use sugar free applesauce instead of the apple pieces! Increase the flaxseed to balance the additional moisture.
Add nuts - Chopped walnuts, pecans or my keto candied pecans.
Change the topping - Make the crumb topping from my keto raspberry muffins or add a simple vanilla glaze from this coconut flour cake.
Substitutions
- Almond flour only - Replace the coconut flour with ¾ cup or 80g additional almond flour.
- Dairy free -Use coconut cream instead of cream cheese.
- Nut free - Sub in a 50/50 blend of sesame flour and sunflower seed flour for the almond flour.

Recipe FAQs
Apples do contain a fair amount of carbs. However, as long as you eat them in moderation, they it can be part of a keto diet. These keto apple cinnamon muffins contain 22.5g or ¼ apple each - that's 5.2g net carbs per muffin.
It's not essential, but leaving the peel on makes the texture more rustic. Apple skins stay firm! I prefer the muffins with peeled apples.
This is a personal choice. All apples work. Cooking apples such as Bramley require more sweetener as they are sour.
Storage
Store the muffins at room temperature for up to 2 days or in an airtight container the fridge for up to 5 days.
All almond flour muffins freeze well! Freeze for up to 3 months.
More Keto Muffin Recipes
Also try my sugar free apple crumble.
Tried this recipe? Give it a star rating below!
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Recipe

Keto Apple Muffins
Video
Ingredients
- 1.5 cup peeled and chopped apples 180g (2 small apples)
- 2 tbsp granulated sweetener for macerating
- 1 teaspoon lemon juice
Batter
- 1 cup almond flour 100g
- ¼ cup coconut flour 30g
- ¼ cup granulated sweetener 50g (use ⅓ cup / 67g for a sweeter muffin)
- 2 tablespoon ground flax 14g
- 1.5 teaspoon baking powder
- 2 teaspoon cinnamon
- ½ cup cream cheese 120g
- 3 eggs large
- 2 tbsp apple cider vinegar
- 1 teaspoon vanilla extract
Topping
- 1 tbsp granulated sweetener
- ½ teaspoon cinnamon
Instructions
- Optional, but recommended: Macerate the apples. Peel, core and chop 2 small apples. Put them in bowl with 1 teaspoon lemon juice and 2 tablespoon sweetener. Stir and let sit for 30 minutes to draw out the liquid.
- Preheat the oven to 180 Celsius / 350 Fahrenheit / 160C fan.
- Blend the eggs and sweetener for 2 minutes until they are frothy and have doubled in volume.
- Add the wet ingredients - cream cheese, apple cider vinegar and vanilla extract. Blend until combined.
- Stir together the dry ingredients in a separate bowl. Add to the egg mix and blend until a smooth batter forms. It will be quite liquid at first, but firms up within 2 minutes as the flax and coconut flour soak up moisture.
- Drain all liquid from the bowl with the chopped apples (it will be about 2 tablespoons). Fold the apples into the muffin batter and fill the batter into 8 paper muffin cups.
- In a small bowl, stir together sweetener and cinnamon. Scatter over the muffins and bake for 30 minutes or until lightly browned.













Roberta
These apple muffins are delicious! Great with a morning cup of coffee. Even my husband likes them and he is a carb fanatic. Thank you Katrin I love your recipes. The ingredients aren't hard to find and the recipes are not complicated.
Natasha
Very nice!
Anne
I am not a lover of coconut flour what should I substitute with?
Katrin Nürnberger
Use more almond flour. The go-to replacement ratio is to use 3x as much almond flour as coconut flour.
Allison Done
Absolutely delicious. Even my carb eating husband loved them!
Ellen
I am dairy intolerant. What can I use instead of cream cheese?
Katrin Nürnberger
You can replace the cream cheese with coconut cream.
marni
Hi, so just to clarify, even though you've extracted the liquid from the apples with the lemon juice and sugar, you're still using the chopped apple as well as the extracted liquid? I'm not clear as to why you extract it if it's all going to be used anyway? Am I missing something 🙂
Katrin Nürnberger
You are using the apples, but not the liquid. 🙂
Cat Collins
Thank you for this, Katrin. I love all things apple!!
Sandra
Is it possible to use a different vinegar?
Katrin Nürnberger
Apple cider vinegar is milder than any other vinegar. I do not recommend replacing it.
Tineke
Very tasty! And easy to make. In the dough I combined cinnamon with punpkin spice. Just ate one with some unsweetend whipped cream and an espresso. Yummy!
Jane
If I were to use applesause instead would I use the same amount?
Katrin Nürnberger
As I mentioned in the post, I think you will need to add more flaxseed to achieve a similar dough consistency because applesauce adds more liquid that is dispersed in the batter rather than in apple pieces. I would add 2 additional tablespoons of flaxseed. Of course, this will all depend on the consistency of the applesauce.
Kevin
Thank you so much. For another great recipe, I can enjoy and stay on my way of eating. I grated the apples this time. Yummy!
Clifford
Perfect day for making apple muffins. I lke the texture of apples with skin on - will this change the recipe if I leave the skin on the apples?
Katrin Nürnberger
Not at all. You'll just add more fibre. And that is always a good thing.