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This has been my go-to pumpkin muffin recipe (we add chocolate chips because yum!) for years. My kids love it. My family always asks for them as soon as the leaves are starting to turn and honestly – we make them well into spring as long as we can find canned pumpkin! Whole wheat sourdough pumpkin muffins are moist, tender and only slightly sweet from pure maple syrup. Made with sourdough discard and soft whole wheat flour (I freshly mill mine), these are a great whole wheat alternative to my other favorite sourdough pumpkin muffins that use an all-purpose flour and more traditional ingredients.
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Why You’ll Love Whole Wheat Sourdough Pumpkin Muffins
- Texture: They are what a pumpkin muffin should be—so moist and delicious! And if you love that same soft texture, you’ll want to try my sourdough pumpkin pancakes and sourdough cornbread muffins too.
- No Refined Sugars: This recipe uses pure maple syrup as a sweetener instead of refined sugar.
- Whole Wheat: You’ll love how these muffins are filled with heart-healthy whole wheat – I like to mill my own for added nutritional benefit! Or try my Spinach Sourdough Banana Muffins that also use whole wheat for more great flavor!
Important Ingredients
- Sourdough Discard – You can use fresh, bubbly sourdough starter if you want. If you don’t mind a more pronounced sourdough flavor, you can use refrigerated discard up to a week or two old. I always use 100% hydration sourdough discard.
- Canned Pumpkin – I use canned pumpkin puree in this recipe (not pumpkin pie filling). If you use homemade pumpkin puree, you’ll need to add some more flour and do your best to blot the pumpkin and strain it from excess liquid.
- Coconut Oil – This is the secret ingredient to making these muffins so soft and tender. They don’t taste like coconut, but it gives it a great texture. Sub any neutral flavored oil or melted butter if you prefer.
- Eggs – Two eggs give these muffins a rich texture and good rise.
- Buttermilk – Buttermilk gives these muffins their fluffy texture and rise.
- Pure Maple Syrup – This recipe doesn’t use any refined sugar, but rather is sweetened with pure maple syrup. Make sure you are using pure maple syrup (not refined pancake syrup!)
- Vanilla Extract – Vanilla balances well with the pumpkin flavor in these muffins.
- Whole Wheat Flour – I like to use soft white whole wheat flour, which I mill myself. You can use any favorite whole wheat flour.
- Cornstarch – Including cornstarch gives these whole wheat muffins a light and fluffy texture.
- Baking Powder – Baking powder helps with the texture and rise of this recipe.
- Spices – In this recipe I love using cinnamon and pumpkin pie spice to really bring out the pumpkin flavor in these muffins.
- Chocolate Chips – I like to use mini or regular semi-sweet chocolate chips for a little extra sweetness and chocolate flavor.
How to Make Whole Wheat Sourdough Pumpkin Muffins
Mix Batter
Wet Ingredients: Add canned pumpkin and melted coconut oil to a medium sized bowl. Mix together until combined. Add the sourdough discard and whisk to combine. Add the eggs, buttermilk, vanilla extract and pure maple syrup. Whisk together until completely combined. Set aside.
Note: Coconut oil can solidify when it comes in contact with cold ingredients. I like to mix it together with room temperature ingredients first until combined. Then I’ll add in colder ingredients and mix quickly to combine together.
Dry Ingredients: In a separate large bowl, add whole wheat flour, cornstarch, baking powder, salt, pumpkin pie spice and ground cinnamon. Fluff together with a fork until combined.
Mix Together: Combine the dry and wet ingredients by pouring the dry ingredients into the liquid ingredients and mixing together until just a few dry streaks remain. Be careful not to over-mix. Add mini chocolate chips and gently mix until spread throughout the sourdough pumpkin muffin batter.
Fill Muffin Tins
Prepare one or two muffin tins by spraying with cooking spray or using muffin or parchment liners. Scoop muffin batter about 3/4 full into each muffin tin each muffin tin. I like to use this scoop and it makes about 16-18 muffins.
Parchment Hack: If using parchment liners, I cut the parchment paper to fit the muffin tin. Then scoop the batter on top of the piece of parchment paper. Take a knife and press down in the corner of the muffin tin to help it sink in.
Bake Muffins
Bake sourdough whole wheat pumpkin muffins at 375ºF for 25-28 minutes until a toothpick is inserted and it comes out clean. Let muffins cool completely (or at least most of the way) before enjoying.
Amy’s Recipe Tip
I love making a mini version of these muffins using a mini muffin tin. This recipe makes about 48 mini pumpkin muffins. They bake for around 12 minutes and are perfect for a quick snack.
Substitutions
This is a healthier version of my sourdough pumpkin muffin recipe. It uses whole wheat flour and non-refined ingredients. If you find yourself making a lot of substitutions or prefer a sweeter muffin, try this recipe for pumpkin sourdough muffins instead.
- Chocolate Chips: Mini chocolate chips add a little extra sweetness to a muffin that is not overly sweet. You can substitute regular sized chocolate chips or even cinnamon chips in this recipe.
- Nuts or dried fruit: You can add chopped nuts or dried fruit to this pumpkin muffin recipe instead of chocolate chips if desired.
- Maple Syrup: Substitute honey for pure maple syrup. You could also substitute sugar, though you may need to add a little extra buttermilk to the batter so it’s not too thick.
- Canned Pumpkin: I use canned pumpkin for this recipe, not homemade pumpkin puree. Homemade puree has a lot more liquid than the canned pumpkin. If you choose to use it, you’ll need to adjust with a little more flour and blotting the pumpkin to get as much excess water out as possible before using.
- Whole Wheat Flour: If you don’t have soft whole wheat flour, you can substitute hard whole wheat or use an all-purpose flour.
- Coconut Oil: Substitute any neutral-flavored oil for the coconut oil in this recipe.
- Buttermilk: Mix together 60 grams sour cream or Greek yogurt AND 55 grams milk. Add in place of buttermilk in this recipe.
How to Store Leftovers
Leftover pumpkin muffins can be stored in an air-tight container at room temperature for 24-48 hours. After that freeze the muffins for freshness – up to 3 months.
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Frequently Asked Questions
Yes. Look for a bag of whole wheat pastry flour for best results with these muffins.
These muffins are only sweetened with the pure maple syrup. They are not overly sweet muffins, so I like the extra pop of sweetness from the mini chocolate chips. If you don’t like sweetness, you can leave them out and substitute nuts or raisins.
No. If you use a good quality soft whole wheat, these are not crumbly muffins. The amount of pumpkin in the recipe also helps them be very moist and delicious – definitely not dry.
Whole Wheat Sourdough Pumpkin Muffins
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Equipment
- parchment paper for lining or muffin liners
Ingredients
- 425 grams canned pumpkin, one, 15 oz can, see recipe notes
- 100 grams coconut oil, melted (1/2 cup) any neutral flavored oil
- 150 grams sourdough discard, heaping 1/2 cup sourdough discard
- 2 large eggs, 100 grams
- 115 grams buttermilk, about 1/2 cup
- 8 grams vanilla extract, about 2 teaspoons
- 240 grams pure maple syrup, about 3/4 cup cup, see recipe notes
- 400 grams soft white whole wheat flour, about 3 cups, see recipe notes
- 20 grams cornstarch, about 2 Tablespoons
- 15 grams baking powder, about 1 Tablespoon
- 9 grams salt , about 1.5 teaspoons
- 8 grams pumpkin pie spice, about 1 Tablespoon
- 8 grams ground cinnamon, about 1 Tablespoon
- 180 grams mini semi-sweet chocolate chips, about 1 cup
Instructions
- Preheat oven to 375ºF. Prepare one or two muffin tins by spraying with cooking spray or using muffin or parchment liners.
- To a medium sized bowl add the canned pumpkin and melted coconut oil. Mix together. Add the sourdough discard and whisk until combined. Add the eggs, buttermilk, vanilla extract and pure maple syrup. Whisk together until completely combined. Set aside.
- To a large bowl, add whole wheat flour, cornstarch, baking powder, salt, pumpkin pie spice and ground cinnamon. Fluff together with a fork until combined.
- Scoop muffin batter about 3/4 full into each muffin tin each muffin tin. You will have some leftover batter to make about 6 extra muffins – 16-18 muffins total.
- Bake muffins at 375ºF for 25-28 minutes until a toothpick is inserted and it comes out clean.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Delicious! 4th time making them in 3 months. I substituted Trader Joe’s caramel chips instead of chocolate chips. Also the 3rd time I forgot the maple syrup completely, didn’t remember until taking them out of the oven. The caramel chips make them so sweet myself and my children didn’t even notice.
Yum! I love the idea of adding caramel chips. Thanks for the idea and review!
These were amazing. Incredibly tender and just the right amount of sweetness. The only substitutions I made were replacing eggs with flax eggs and soy milk/lemon juice for the buttermilk.
Thanks for the review – I’m glad you love the recipe! And thanks for the substitution ideas!
So good and soft even with normal store bought whole wheat flour. I love that it’s healthy with the whole wheat and still delicious!
Thanks for the review! Glad you love the recipe.
Amy.. these are AMAZING! My goal is to not cook with refined sugar and these hit the spot. I added 1/2 cup applesauce which helps sweeten and keep them moist. I also prefer to cook with honey, so I used honey instead. Otherwise I followed the recipe and they turned out perfect. My family gobbled these up! I will be adding these to my rotation. Thank you
So glad you loved these!
These were a little too healthy for my liking. I suppose that’s on me, or on the rest of the internet for posting pumpkin muffins with lots of sugar and white flour. Either way, I think next time I will give the version with cinnamon chips from your site a try.
Thanks for sharing your thoughts! They definitely are meant to be a “healthy” pumpkin muffin with no refined sugar. I think you guys would really like the recipe with all-purpose flour and cinnamon chips (or chocolate chips if you prefer): https://amybakesbread.com/sourdough-pumpkin-muffins-with-cinnamon-chips/
These muffins are so good! I LOVE that you made them with freshly milled flour and maple syrup for the sweetener! They really are a great tasting healthy muffin!
So glad you loved these! They are definitely my go-to for a healthy sourdough pumpkin muffin 🙂
is there something i can use instead of cornstarch or can this just be omitted with adding a little extra flour?
You can leave it out and sub extra flour
You can leave out the cornstarch and add in the extra flour.
Have you ever tried putting nuts in the pumpkin muffins.
I haven’t. My kids are partial to chocolate chips – and the muffin itself is not very sweet with just the maple syrup to sweeten it. But I think nuts would taste great in there – just haven’t tried it.
My kids beg for these whole wheat sourdough pumpkin muffins every year. Not super sweet, but they are soft, moist and tender and I love making them with freshly milled flour.