These quick and easy gluten-free sourdough chocolate chip muffins are a delicious breakfast or on the go snack. Made all in one bowl, they couldn’t be easier! They are made with almond flour and sweetened with honey so they won’t spike your blood sugar like the average muffin. Slightly tangy from the sourdough discard and yogurt with just enough sweetness from the honey and chocolate chips.
Ingredients You Will Need
Gluten-Free Sourdough Discard – this recipe is a great opportunity to use up any extra starter you have on hand. But, don’t worry, if you don’t have extra you can still use active discard as well. The starter adds just a touch of sourness to the muffins without it being too noticeable.
Large Eggs – I like to use organic pasture-raised eggs if possible, but any eggs that you have on hand will work just fine. The eggs act as the binder in this recipe since you don’t have gluten to do the job.
Plain Yogurt – You want to make sure it is plain yogurt and not Greek yogurt as Greek yogurt is too thick for this recipe. If you only have Greek yogurt on hand, you can thin it out with a little milk. I like to use my homemade 24 hour instant pot yogurt for this.
Honey – I like to use organic raw unfiltered honey, but any honey you have on hand will work.
Melted Butter – You can’t go wrong with butter! This just helps to make these muffins extra delicious and rich. Make sure you let the butter cool a bit before add it with the eggs so they don’t start to cook!
Vanilla Extract – Pure vanilla extract is best if you have it.
Almond Flour – I love using almond flour in sweet recipes. I actually prefer it over regular flour now. Almond flour has so many health benefits as well, so you can feel better about eating your sweet treat. My favorite brand is Anthony’s brand on Amazon.
Baking Soda – baking soda helps to give these muffins their rise.
Salt – this is important in all recipes to bring out the flavor! I use Diamond Crystal Kosher Salt.
Mini Chocolate Chips – I use Lily’s brand mini chocolate chips. I like the mini chocolate chips because I feel like they don’t weigh the muffins down like regular chocolate chips. If you don’t have them, regular chocolate chips will work though.
Directions
Combine the Wet Ingredients – to a large mixing bowl add the gf sourdough discard, eggs, yogurt, honey, melted and cooled butter, and vanilla extract. Whisk well to combine.
Add the Dry Ingredients – add almond flour, baking soda, and salt. Stir with a rubber spatula until fully incorporated, being careful not to over mix.
Add the Chocolate Chips – add the chocolate chips and gently stir to combine.
Cover and Refrigerate – cover the bowl and place it in the refrigerator for up to 24 hours. You can skip this step if you like, but I think it’s worth the wait. I also like the fact that I can break up the process and it makes it easy to just pop them in the oven the next morning.
Preheat Your Oven – when you’re ready to bake, preheat your oven to 350 degrees F.
Scoop and Bake – line a 12 cup muffin tin with parchment liners and scoop the batter into the muffin cups. I like to use a muffin scoop, but a spoon works too.
Bake – bake the muffins for 20 minutes until lightly browned and a toothpick inserted in the middle comes out clean.
Cool and Serve – let the muffins sit in the muffin tin for 10 minutes before removing. Serve and enjoy!!

Want to Make These Paleo?
You can easily make these muffins paleo if you like. You will need to use a grain-free sourdough starter. You can then swap out coconut oil or avocado oil for the butter and swap out dairy free yogurt or dairy free milk for the yogurt.
Enjoy!
I hope you enjoy these gluten-free sourdough discard chocolate chip muffins as much as my family does! Please let me know if you have any questions in the comments.

Gluten-Free Sourdough Chocolate Chip Muffins
Equipment
- 1 12 cup muffin pan
Ingredients
- 74 g gluten-free sourdough discard
- 3 large eggs
- 22 g plain yogurt
- 113 g honey
- 30 g melted butter unsalted
- 1 tsp pure vanilla extract
- 168 g blanched almond flour
- 3/4 tsp baking soda
- 1/4 tsp salt
- 128 g mini chocolate chips
Instructions
- To a large mixing bowl, add the starter, eggs, yogurt, honey, butter, and vanilla extract. Whisk well to combine.74 g gluten-free sourdough discard, 3 large eggs, 22 g plain yogurt, 113 g honey, 30 g melted butter, 1 tsp pure vanilla extract
- Add the almond flour, baking soda, and salt. Stir to combine with a rubber spatula. Then add the chocolate chips and continue stirring until just combined.168 g blanched almond flour, 3/4 tsp baking soda, 1/4 tsp salt, 128 g mini chocolate chips
- For the most flavorful muffins, cover the bowl and place in the refrigerator for up to 24 hours.
- When you are ready to bake, preheat your oven to 350 degrees F.
- Line 12 muffin cups with parchment liners. Spoon the batter into the parchment liners with a muffin scoop or a spoon.
- Bake for 20 minutes until lightly browned and a toothpick inserted comes out clean.
- Let sit for 10 minutes before removing and place on wire rack to cool. Serve warm or at room temperature.
Notes
- You can substitute milk of any kind for the yogurt.
- You can substitute melted coconut oil or avocado oil for the butter.
- If you don’t want to wait to bake these, you can bake them right away after mixing the batter.








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