Potato Flake Sourdough Apple Muffins

These potato flake sourdough apple muffins are tender, sweet and topped with a cinnamon crumb topping—perfect for fall mornings or anytime you’re craving something homemade with fresh apples. 

If you’ve been looking for a new recipe to use your potato flake starter, these sourdough apple cinnamon muffins are the perfect recipe to try! 

These never last long around my house. Sweet, lightly spiced, and topped with a buttery crumb, they’re perfect for breakfast, paired with afternoon coffee, or a treat for any time of the day. This is one of those sourdough muffin recipes that’s so simple, you can’t believe how delicious it is. 

It’s a great recipe to use up  leftover sourdough starter (aka discard) and still gives the muffins a rich flavor and is easier to digest thanks to the gentle fermentation process. Pair that with the crisp apples and cinnamon-it’s the perfect bite. I used granny smith apples this time, but any fresh apples you have on hand will do.

The batter is mixed in one large bowl, and after a rest on the counter for 8–12 hours, you’ve got yourself a muffin with a tender crumb that rivals any bakery-style muffin.

This post may contain affiliate links through amazon, which means I may make a small commission at no extra cost to you. When you make a purchase through my link, you help me to keep Little Tennessee Home up and running! Thank you for your support! See my full disclosure here.

Tools you will need:

Large mixing bowl

Rubber spatula

Measuring cups and spoons

12 cup Muffin pan

Muffin liners (These parchment liners are my favorite!)

1/4 measuring cup or 1/4 cup cookie scoop to scoop the batter evenly into the muffin tin

Ingredients

Bulk Ferment:

• 2 cups all-purpose flour (260 grams)
• 1 cup raw organic sugar (213 grams)
• ½ cup melted unsalted butter (not hot!) (108 grams)
• ½ cup potato flake discard (130 grams)
• 2 large eggs
• ¼ cup plain yogurt (67 grams) — or Greek yogurt

After Fermentation:

• 1 teaspoon baking soda (Add 1 teaspoon baking powder too if you’re skipping the long ferment)
• ½ teaspoon salt
• 1 teaspoon vanilla extract
• 1½ teaspoons cinnamon (or sub with apple pie spice if you’re feeling festive)

Add-Ins:

• 1½ cups diced fresh apples (about 2 granny smith apples, peeled and cored)

Crumb Topping:

• ½ cup all-purpose flour
• ¼ cup raw sugar
• ¼ cup brown sugar
• 4 tablespoons melted butter
• 1 teaspoon cinnamon
  (Optional: sprinkle a bit of turbinado sugar on top for sparkle and crunch)

Instructions for Potato Flake Sourdough Apple Muffins

Mix the Wet Ingredients:

In a large bowl, whisk together the sugar and eggs until smooth. Add the yogurt, melted unsalted butter, and potato flake starter (active or discard). Stir until everything is well combined.

Combine with Dry Ingredients:

Add in the flour and fold it into the mixture using a spatula. Don’t overmix. Cover the bowl with plastic wrap or beeswax wrap, and let it rest at room temperature for 8–12 hours. This step allows the batter to ferment gently, improving both flavor and digestibility by breaking down some of the phytic acid in the flour.

Prepare to Bake:

Preheat the oven to 400°F (oven temperature is important for getting those domed muffin tops). Line a prepared muffin tin with muffin cups and lightly spritz with nonstick spray if desired.

Make the Crumb Topping:

In a small medium-sized bowl, mix the topping ingredients until crumbly. Set aside.

Finish the Batter:

After fermentation, stir in the baking soda, cinnamon, salt, and vanilla extract (or swap in vanilla bean paste for a more intense flavor). Peel and dice the apples. Fold the diced apples gently into the batter.

Fill the Muffin Cups:

Using a 1/4 cup large cookie scoop, spoon heaping ¼ cup portions of batter into each cup. Top generously with the crumb mixture. This recipe makes about 15 delicious muffins, so bake in batches if needed.

Bake:

Place muffins in the oven and reduce heat to 375°F. Bake for about 15 minutes, or until the tops are golden brown and a toothpick comes out clean.

Cool:

Let muffins cool in the tin for 5 minutes, then transfer to a wire rack.

Storage & Tips

• Store muffins in an airtight container at room temperature for 2–3 days, or in the refrigerator for up to a week. Heat them in the microwave for a few second before eating.
• These freeze well too—wrap individually and store in a freezer-safe container.
• Want a more whole grain flavor? Swap equal amounts of flour for whole wheat flour or even bread flour if needed for a heartier bite.
• This recipe works great with both active sourdough starter and discard.

Long fermenting vs. baking immediately

I almost always choose to long ferment when using my potato flake sourdough starter because it makes the grains so much easier to digest and easier for your body to absorb the nutrients.

Sometimes, though, you have some discard and you need to whip up something for breakfast or to take to a gathering and don’t have time to wait. Thankfully, this recipe can be made without long fermenting! The trick is to add in baking powder in addition to the baking soda to make sure that your muffins rise! The potato flake starter won’t have time to ferment any grains, but it will still add flavor to your muffins!

Fermenting potato flake sourdough with eggs at room temperature:

While everyone must make this decision for themselves, I am comfortable allowing dough that includes eggs to ferment at room temperature. In a very short explanation, the good bacteria in the starter that causes the fermentation, also prevents bad bacteria from growing. I have always allowed my dough that includes eggs, to ferment at room temperature, without any issues.

However, I suggest that you make the decision on your own if you would like to do this or not. If you do not feel comfortable, you can simply mix all of the ingredients except the eggs and allow it to ferment, adding the eggs in after the long fermentation. It will be difficult to incorporate, but it can be done with patience and determination!

Pin it for later and share it with a friend:

Whether you’ve just come back from apple picking or are simply craving that cozy, sweet-tart flavor of an apple muffin recipe, this is the best way to enjoy the sweetness of apples in a perfect muffin.

If you give this recipe a try, I would greatly appreciate if you came back and gave it a 5-star review! It helps me out so much! 

I also love seeing all of the delicious creations you make! Share your photo over on instagram or facebook and give me a tag @littletennesseehome