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Healthy Sourdough Cinnamon Muffins Recipe

These sourdough cinnamon muffins have quickly become a family favorite. The sweetness paired with the subtle spice of the cinnamon and nutmeg make for a soft and satisfying muffin.

muffins on a plate with a knife and butter

It’s no secret that our family loves breakfast. From our fluffy pancakes to our simple pumpkin sourdough bread, we all look forward to that comfort in the morning.

Sourdough has so many benefits, but one is that anything that has a mature sourdough starter in it is easier to digest and makes for better nutrition absorbption.

I have had my starter for several years now and try to slip it into any recipe I can.

These cinnamon muffins were the latest to be filled with the health benefits of sourdough.

So, while these are filled with gut loving bacteria, they are also fluffy and filled with incredible flavor!

muffins sliced in half on a counter

Why you’ll love these Sourdough Cinnamon Muffins

  • These muffins are sweet and spicy
  • They are delicious and perfect for breakfast or a healthy snack
  • You will have a muffin full of great health benefits by including the sourdough
  • Sourdough discard or mature sourdough can be used in this recipe
  • Sourdough cinnamon muffins can be made ahead of time and kept in the refrigerator or freezer
  • The texture of these muffins is so satisfying as they are soft and fluffy on the inside and a nice, dense outside
  • This recipe is a dump and bake recipe, just like my overnight oatmeal bake for kids, that doesn’t require any fancy gadgets or much time
flour in a bowl with eggs and a wire whisk

Why these Sourdough Cinnamon Muffins work

This is a straight forward recipe that uses basic ingredients every home cook has.

As with any good muffin recipe, you start with your wet ingredients in one bowl and you combine them with your dry ingredients.

You will want to mix until just combined so that you don’t overwork the batter.

How to make Sourdough Cinnamon muffins

  • You will want to feed your starter a few hours (or up to ten hours) before you need it for this recipe.
  • Add to your starter the wet ingredients and stir until combined.
  • In a large mixing bowl, combine all of your dry ingredients.
  • Pour the wet ingredients into the dry ingredients and mix.
  • Fill muffin tins 1/2 way full and bake.
rehydrating dry sourdough starter with flour and a digital scale

Ingredients for Sourdough Cinnamon Muffins

  • All-Purpose Flour– An all-purpose flour was used in this recipe, but you can use other flours that you like to bake with.
  • Sourdough Starter– This recipe will work with a sourdough discard, but I prefer making a quick levain from my dry sourdough starter (if you don’t know what I’m talking about, you must check it out!) and using that in this recipe.
  • Baking Powder and Baking Soda– These act as leavening agents when combined with the wet ingredients.
  • Salt– Everything sweet needs a bit of salt to bring out the flavor.
  • Cinnamon and Nutmeg– The spices of the recipe that will make everyone love this recipe.
  • Butter– Melted and delicious
  • Brown Sugar and White Sugar– I like the combination of the two sugars because they do offer different flavor profiles. Use what you have on hand. I oftentimes swap out these for maple sugar, coconut sugar, or sucanat.
  • Vanilla– To give some depth of flavor
  • Milk– You may use heavy cream if you want a richer muffin, but I use whole milk.
  • Egg– To give some structure to the batter
fluffy cinnamon muffins on a plate

How to get a tall cinnamon muffin

If you love those tall, full muffins then you will love this recipe.

Cinnamon muffin batter is thick and dense, which creates a tall muffin that tastes amazing.

If you’re wanting a recipe that creates a tall muffin, this is the recipe for you!

sliced muffins on a blue and white plate with a knife

Cinnamon Muffin Crumb Topping

If you want to dress up your muffin a bit, you can make this simple crumb topping that I like to put on lots of our muffin recipes.

These muffins are amazing alone, but you add a streusel on top?? Downright divine! This streusel is a basic streusel you can use on most breakfast breads.

  1. Add 1/2 cup all-purpose flour, 1/2 cup brown sugar, and 1/2 cup old fashioned oats to a medium mixing bowl.
  2. To that mixture, add 1/2 teaspoon salt and 3/4 teaspoon Baking Powder.
  3. Add 5 tablespoons of melted butter to the bowl and mix well.
  4. Top muffin batter with the streusel and bake according to muffin instructions.
sourdough muffins on a counter with butter

Can I freeze Cinnamon Muffins?

All breakfast breads can be frozen and these muffins freeze beautifully. It is best to let them fully cool and then you can put them in a plastic ziplock to freeze them.

They stay good for 3-4 months in the freezer. Allow muffins to come to room temperature before eating.

muffins on a plate with dried hydrangeas

Can these Sourdough Cinnamon Muffins be made into a bread loaf?

If you would rather have a loaf of cinnamon bread, grease a bread loaf pan with butter and pour the batter into the loaf pan.

Bake at 350°F for 60 minutes, or until a toothpick comes out clean when inserted in the middle.

The bake time will be determined by how high you fill the loaf pan. I fill mine 2/3 high and it requires an hour of bake time.

If you fill yours lower, it’ll bake faster. If you fill it higher, it’ll require extra baking time.

chunks of chocolate and pecans on a table

Variations for Cinnamon Muffins

  • Add Nuts- Add nuts for a bit of chew to these muffins. I prefer walnuts or pecans.
  • Dried cranberries- Cranberries give this sweet muffin a tartness and a hint of “chocolate cherry” flavor when the cranberry and cinnamon are mixed.
  • Chocolate chunks- Chocolate chips are are a great addition to any muffin
  • Shredded Zucchini- You can shred 1/2 cup of zucchini and press the liquid out of it with a towel.

Tips for this recipe

  • Make sure to bake the muffins until they are fully baked. Test their doneness by sticking a toothpick in the center of one of the muffins. If it comes out clean, then the muffins are done.
  • Fill your muffin tins 3/4 of the way full. You don’t want to overfill the muffin tins or the batter will outgrown the tin in the oven when it’s baking. Allow some room for it to rise.

muffins sliced in half with a knife that has butter on it

Frequently asked questions

What is the secret to tall, fluffy muffins?

If you want tall, fluffy muffins be sure to have your egg, butter, and milk at room temperature before you start your batter. Fill your muffin cups all of the way to the top of the tin with a thick muffin batter. Blast the muffins in the oven at a high temperature (400°F) for 5 minutes to create a “rise” to the muffin and then reduce the temperature to what the recipe card calls for and bake until the muffins are done.

What makes a muffin moist?

The best way to get a moist muffin is to use liquids, such as melted butter and milk. Plus, you need to make sure you don’t overmix the batter. Stir it until it is combined and then stop mixing.

My Favorite Kitchen Things

Cooking Pans
cinnamon muffins sliced on a plate

Healthy Sourdough Cinnamon Muffins

Liz Quick
These sourdough cinnamon muffins have quickly become a family favorite. The sweetness paired with the subtle spice of the cinnamon and nutmeg make for a soft and satisfying muffin.
5 from 3 votes
Prep Time 2 hours 12 minutes
Cook Time 18 minutes
0 minutes
Total Time 2 hours 30 minutes
Course Breakfast
Cuisine American
Servings 12 muffins
Calories 100 kcal


  • 1 muffin tin


  • cup all purpose flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • teaspoons cinnamon
  • ½ teaspoon ground nutmeg
  • ¼ teaspoon salt
  • 4 tablespoons butter, melted
  • ¼ cup brown sugar
  • ½ cup white granulated sugar
  • 1 teaspoon vanilla
  • ¼ cup milk
  • 1 large egg
  • 1 cup sourdough starter, fed and bubbly


  • Feed your sourdough starter 2-10 hours before you make this recipe so it will be nice and bubbly. If you don't feed it, it will still be fine, you just won't have grains that are as broken down.
  • Preheat your oven to 400°F.
  • Whisk the dry ingredients together in a large mixing bowl: flour, baking powder, baking soda, cinnamon, nutmeg, and salt.
  • Add the melted butter, brown sugar, white sugar, vanilla extract, milk, and egg in a medium mixing bowl and mix well with a large spoon.
  • Pour in your sourdough starter with the wet ingredients and mix well with a wooden spoon.
  • Add your wet ingredients to your dry ingredients and mix until just combined.
  • Add muffin liners to a muffin tin or spray with non-stick spray. Fill the cups ½ way full and place in a preheated oven for 20 minutes, or until the muffins bounce back when tapped on top.


How to get a tall cinnamon muffin

If you love those tall, full muffins then you will love this recipe.
Cinnamon muffin batter is thick and dense, which creates a tall muffin that tastes amazing.
If you’re wanting a recipe that creates a tall muffin, this is the recipe for you!
Keyword cinnamon muffins, sourdough cinnamon muffins, sourdough muffins

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  1. 5 stars
    I just took them out of the oven, and they look marvelous!! I am allergic to egg, so I substituted Just Egg. They smell amazing, and I can’t wait to try them!!

  2. You mentioned that you could use honey in place of sugar in these muffins…Do you know what the measurement would be and if any other ingredients would need to be altered to compensate? They are super yummy!

    1. I would sub the same measurements, but do keep in mind that honey is sweeter than sugar, so depending upon your flavor preferences you might sub a little less than what is called for in the recipe.

  3. 5 stars
    So delicious! Perfect amount of cinnamon. Even my picky kiddos love these muffins. I like to enjoy them with a hot cup of coffee in the morning

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