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These Pumpkin Chocolate Chip Muffins are soft, squishy and packed with chocolate chunks! The sweet muffins are delicately flavoured with pumpkin, cinnamon and nutmeg with plenty of chocolate, making them the perfect bake for autumn. And coeliac-safe!

Notes On These Pumpkin Choc Chip Muffins
💛 Soft, squishy pumpkin muffins with fat chunks of chocolate, and completely gluten free, using easy-to-find ingredients you probably already have at home.
💛 Gluten free bakes can often have a bad rep for being dry – I’ve found using pumpkin really helps retain the moisture as well as adding flavour and colour!
💛 These are a great meal prep breakfast option – you can bake a batch up to last the week and they’re not too sweet. Plus you’re even getting some veg in with brekkie!
Table of Contents

Ingredients and Substitutions
There’s a printable recipe card below for these pumpkin chocolate chip muffins with the full quantities. But here are the main ingredients and ideas for any swaps.
- Pumpkin Puree: You can either use canned pumpkin puree or make your own pumpkin puree – it’s really cheap and easy to make when pumpkins are in season.
- Light Brown Sugar: Swap for caster sugar if needed.
- Vegetable Oil: or any other neutral-tasting oil.
- Eggs
- Yoghurt: Use a natural or Greek yoghurt – or a dairy free alternative if needed.
- Plain Gluten Free Flour: I usually use the FREEE flours, but any plain or all purpose gluten free flour blend should work.
- Xanthan Gum: You can omit this if your flour blend already contains it.
- Baking Powder: Not all baking powder is gluten free – use my gluten free baking powder guide to be sure you’re using a coeliac-safe brand.
- Bicarbonate of Soda: Also known as baking soda in the US.
- Spices: I use a blend of cinnamon and nutmeg. A little ginger or cloves would also add a nice touch, or even some pumpkin spice.
- Dark Chocolate Chips: Ensure you use a gluten free brand. For sweeter muffins use milk chocolate drops, or use a dairy free chocolate if needed.

How to Make Pumpkin Chocolate Chip Muffins
There’s a printable recipe card below with the method. But here are some step-by-step photos to show you how easy these pumpkin chocolate chip muffins are to make.






Storing and Freezing Instructions
TO STORE: These pumpkin chocolate chip muffins will keep for up to a week in an airtight container. Keep them at room temperature – the fridge makes them go stale.
TO FREEZE: You can freeze these and defrost at room temperature to eat. They’re great as a meal prep breakfast option, just defrost overnight, grab and go!
Pumpkin Chocolate Chip Muffins Recipe
Equipment
Ingredients
- 200 g pumpkin puree, (canned, or homemade)
- 200 g light brown sugar
- 120 ml vegetable oil, (or other neutral-tasting oil)
- 2 large eggs
- 60 g yoghurt, (natural or Greek yoghurt)
- 250 g plain gluten free flour
- 0.25 tsp xanthan gum
- 3 tsp gluten free baking powder
- 1 tsp bicarbonate of soda
- 2 tsp ground cinnamon
- 0.25 tsp ground nutmeg
- 165 g dark chocolate chips
Instructions
- Preheat the oven to 200C / 180C Fan / Gas Mark 6 / 365F and line a 12-hole muffin tin with 12 muffin cases.
- Add the gluten free flour, xanthan gum, baking powder, bicarbonate of soda, cinnamon and nutmeg to a large bowl and mix well to combine.
- To a large mixing bowl, add the pumpkin puree, brown sugar, vegetable oil, eggs and yoghurt. Mix with an electric mix until combined.
- Add in the dry ingredients and mix again until just combined – don’t overmix.
- Pour in the chocolate chips (I reserve a small amount to put on top of the muffins before baking) and fold them in, using a wooden spoon.
- Divide the mixture between the muffin cases – you want them around three-quarters full, do not overfill them too much as they should rise a lot.
- Dot the extra choc chips on top of the muffins. Place in the oven and bake for 5 minutes.
- After 5 minutes, DO NOT OPEN THE DOOR, but turn the oven down to 180C / Fan 160C / Gas Mark 4 / 320F and cook for another 18-20 minutes until the muffins are well risen and golden on top.
- Remove from the oven and cool before eating. Great for a lunchbox snack or Fall breakfast on-the-go!
Video
Notes
- To make this recipe dairy free, swap the yoghurt for a dairy free yoghurt and ensure you use dairy free chocolate.
Nutrition
Got Leftovers? Make These!
Once you’ve made these gluten free pumpkin chocolate chip muffins I have plenty of ways for you to use any leftovers to ensure nothing goes to waste.
- For Leftover Pumpkin: Try making my Gluten Free Pumpkin Roll for a tasty dessert, Pumpkin Banana Muffins for a simple breakfast on-the-go or Gluten Free Pumpkin Bread for an autumnal baking treat. For savoury options, try my Creamy Pumpkin Pasta or easy Roasted Pumpkin Soup.
More Gluten Free Muffin Recipes
If you like this pumpkin chocolate chip muffins recipe then make sure you check out these other gluten free muffin recipes too…
- Gluten Free Blueberry Muffins
- Gluten Free Choc Chip Muffins
- White Chocolate Raspberry Muffins
- Lemon and Poppyseed Muffins
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