Moist Pumpkin Oat Muffins with Freshly Milled Flour
If you love all things pumpkin, these moist pumpkin oat muffins with freshly milled flour deserve a spot on your fall baking list! Made with pumpkin puree, old-fashioned oats, and warm pumpkin spice, they’re wonderfully moist and easy to customize with monk fruit sweetener, dark chocolate chips, or your favorite add-ins.

Reader Summary
Here’s what you’ll find in this recipe:
- Moist, tender muffins: Pumpkin puree and unsweetened applesauce help keep these muffins soft.
- Freshly milled flour: A delicious way to use soft white wheat in your fall baking.
- Sweetener options: Use monk fruit sweetener, granulated sugar, or coconut sugar.
- Optional add-ins: Customize your muffins with chocolate chips, nuts, or pumpkin seeds.
- Freezer-friendly: Make a batch ahead of time and enjoy a warm muffin whenever the craving strikes.
*This post may contain affiliate links, which means I may earn a small commission if you make a purchase through my links, at no additional cost to you. Thank you for supporting Our Manor On Main and helping me continue sharing recipes and inspiration!
If you are looking to make ALL the pumpkin things this season, check out some of these other favorites on the blog: Cozy Homemade Pumpkin Butter for Fall Mornings, Pumpkin Spice Pancakes with Cinnamon Sugar Honey Butter, Sourdough Pumpkin Cinnamon Rolls with Cream Cheese Pumpkin Icing, or enjoy the ultimate Fall-in-a-cup trio, cold brew coffee with homemade pumpkin sauce topped with pumpkin cold foam!

A Little Story Behind These Pumpkin Oat Muffins
If you’ve spent much time on my blog, you’ve probably figured out that I’m a pumpkin freak. Some people go crazy for apple season, but I’m over here dreaming about all the pumpkin things I can bake as soon as fall rolls around!
I already have a recipe for freshly milled pumpkin muffins using sourdough, but I wanted to make something a little different. I thought adding old-fashioned oats would give these muffins a heartier texture while keeping them really moist and tender.
And that’s how these pumpkin oat muffins came to be! I love that you can make them your own, whether you prefer them plain, with dark chocolate chips folded into the batter, or topped with a sprinkle of pumpkin seeds.
And if you really want to make them extra delicious, serve a warm muffin with my homemade cinnamon sugar honey butter. Trust me, that combination is hard to beat!
Why You’ll Love This Recipe
They’re wonderfully moist. Pumpkin puree and unsweetened applesauce add moisture without needing a lot of oil.
They’re full of fall flavor. Homemade pumpkin spice and cinnamon give these muffins that cozy flavor I look forward to every autumn.
You can customize the sweetness. I used monk fruit sweetener, but you can substitute regular granulated sugar or coconut sugar if you prefer.
They work with all your favorite add-ins. Dark chocolate chips are delicious, but white chocolate chips, chopped nuts, and pumpkin seeds are great options, too.
They’re perfect for the freezer. Bake once, freeze a batch, and warm up a muffin whenever you want a quick breakfast or snack.

Ingredients You’ll Need
- Flour: I used 1 cup of freshly milled soft white wheat flour. If you’re new to freshly milled flour, soft white wheat is a lovely option for tender baked goods. I’ll go into more detail later in this post!
- Pumpkin puree: Use pure canned pumpkin, not pumpkin pie filling.
- Old-fashioned rolled oats: These add texture and a hearty oat flavor.
- Sweetener: I used ½ cup of Monk fruit to make it sugar-free. Choose a granulated product suitable for baking and follow its sugar-equivalency guidance if it isn’t a one-to-one substitute.
- Unsweetened applesauce: Four ounces help keep the muffins moist.
- Eggs: Two large eggs help bind the ingredients together.
- Avocado oil: Adds moisture without overpowering the pumpkin flavor.
- Pure vanilla extract: Adds warmth and rounds out the flavors.
- Homemade pumpkin spice: I used my own homemade pumpkin spice blend, and you can find the recipe here: Homemade Pumpkin Spice Mix Recipe (Perfect for Pies, Coffee, and More)
- Ground cinnamon: Adds another layer of cozy fall flavor.
- Baking soda and baking powder: These work together to help the muffins rise.
- Salt: Balances the sweetness and brings out the other flavors.

Optional Add-Ins
The chocolate chips are entirely optional! I tend to measure those with my heart, but here are some starting points if you’d like a little guidance.
- Dark chocolate chips: Start with ½ cup for pockets of chocolate throughout the muffins.
- White chocolate chips: Use ½ cup for a sweeter variation.
- Chopped pecans or walnuts: Add ¼ cup for a little crunch.
- Pumpkin seeds: Sprinkle 2–3 tablespoons over the tops before baking.
- A combination: Try dark chocolate chips with a few chopped pecans for a delicious fall-inspired muffin.
If you’re using several add-ins, keep the total amount moderate so the batter can support them. You can also leave everything out for a simple pumpkin oat muffin.
How to Make Pumpkin Oat Muffins
1. Preheat the Oven
Preheat your oven to 350°F. Grease a standard muffin tin with a little avocado oil or coconut oil, or line the wells with muffin liners.
2. Mix the Dry Ingredients
In a medium bowl, whisk together the freshly milled flour, homemade pumpkin spice, ground cinnamon, salt, baking soda, and baking powder until evenly combined.

3. Combine the Wet Ingredients
In a separate, larger bowl, combine the pumpkin puree, monk fruit sweetener, unsweetened applesauce, eggs, avocado oil, and vanilla extract. Stir until the mixture is smooth and well combined.

4. Combine the Wet and Dry Ingredients
Add the dry ingredients to the wet ingredients. Stir gently until the flour is incorporated, taking care not to overmix the batter.

5. Fold in the Oats and Optional Add-Ins
Fold in the old-fashioned rolled oats. If you’re adding dark chocolate chips, white chocolate chips, or chopped nuts, gently stir them in now.

6. Fill the Muffin Tin
Divide the batter among approximately 10 prepared muffin wells. If you’re using pumpkin seeds, sprinkle a few over each muffin.

7. Bake
Bake at 350°F for approximately 25 minutes. Since ovens can vary, begin checking toward the end of the baking time.
Insert a toothpick into the center of a muffin. If it comes out without wet batter, the muffins are ready. Melted chocolate may leave a little residue, so try to test a spot without a chocolate chip.

8. Cool and Enjoy
Allow the muffins to cool in the pan for several minutes before carefully transferring them to a wire rack.
Enjoy one while it’s still a little warm, especially with a pat of homemade cinnamon sugar honey butter!

Pumpkin Oat Muffins with Freshly Milled Flour
Ingredients
- 1 cup freshly milled white wheat Can use all-purpose
- 2 tsp pumpkin spice blend I use homemade!
- 1/2 tsp ground cinnamon
- 1/2 tsp salt
- 1 tsp baking soda
- 1/2 tsp baking powder
- 1 cup canned pumpkin puree
- 1 cup sugar or coconut sugar I used Monkfruit to make it refined sugar-free
- 4 oz unsweetened applesauce
- 1 tsp vanilla extract
- 2 tbsp avocado oil Can use coconut oil or EVOO
- 2 large eggs
- 2/3 cup old-fashioned rolled oats
Instructions
- Preheat your oven to 350°F. Grease a standard muffin tin with a little avocado oil or coconut oil, or line the wells with muffin liners.
- In a medium bowl, whisk together the freshly milled flour, homemade pumpkin spice, ground cinnamon, salt, baking soda, and baking powder until evenly combined.
- In a separate, larger bowl, combine the pumpkin puree, monk fruit sweetener, unsweetened applesauce, eggs, avocado oil, and vanilla extract. Stir until the mixture is smooth and well combined.
- Add the dry ingredients to the wet ingredients. Stir gently until the flour is incorporated, taking care not to overmix the batter.
- Fold in the old-fashioned rolled oats. If you're adding dark chocolate chips, white chocolate chips, or chopped nuts, gently stir them in now.
- Divide the batter among approximately 10 prepared muffin wells. If you're using pumpkin seeds, sprinkle a few over each muffin.
- Bake at 350°F for approximately 25 minutes. Since ovens can vary, begin checking toward the end of the baking time.Insert a toothpick into the center of a muffin. If it comes out without wet batter, the muffins are ready. Melted chocolate may leave a little residue, so try to test a spot without a chocolate chip.
- Allow the muffins to cool in the pan for several minutes before carefully transferring them to a wire rack.Enjoy one while it's still a little warm, especially with a pat of homemade cinnamon sugar honey butter!
How to Serve Pumpkin Oat Muffins
There are so many delicious ways to enjoy these muffins!
- With cinnamon sugar honey butter: This is my favorite serving suggestion. Spread a little of my homemade cinnamon sugar honey butter over a warm muffin and let it melt into all those pumpkin-spiced nooks and crannies.
- With your morning coffee: A pumpkin muffin and a hot cup of coffee make a lovely fall breakfast. Add a little Pumpkin Sauce to your coffee to give it a sweet fall twist!
- As an afternoon snack: Keep one on hand when you want something homemade with a little pumpkin spice.
- With a little extra crunch: If you left the nuts out of the batter, sprinkle some chopped pecans over the butter when serving.

How to Store Pumpkin Oat Muffins
At Room Temperature
Once the muffins have cooled completely, store them in an airtight container at room temperature for about 2 days. Keep them in a cool, dry spot and avoid sealing them while they’re still warm, since trapped steam can make the tops damp.
For the best texture, I prefer enjoying them fresh or freezing the extras rather than keeping them on the counter for several days.
Should You Refrigerate Pumpkin Muffins?
You generally don’t need to refrigerate these muffins if you’re going to eat them within a couple of days. Refrigeration can make muffins lose some of their soft texture and seem drier.
If your kitchen is particularly warm or humid, or you need to keep them longer, refrigerating them is an option. Store them in an airtight container and warm them briefly before serving. For longer storage, I recommend freezing instead.
How to Freeze Pumpkin Oat Muffins
These muffins freeze beautifully, which makes them perfect for preparing ahead!
- Let the muffins cool completely.
- Place them in a freezer-safe bag or airtight container. For extra protection against freezer burn, wrap them individually before placing them in the bag.
- Label and date the container, then freeze for up to 3 months for the best quality.
How to Reheat Frozen Pumpkin Muffins
When you’re ready for a muffin, remove one from the freezer and unwrap it if necessary.
- Microwave: Heat for about 30 seconds to start. If the center is still cold, continue in short intervals until warmed through. A larger or very cold muffin may need closer to a minute.
- Thaw first: Let the muffin thaw at room temperature, then warm it briefly if you’d like.
Be careful when biting into a microwaved muffin, especially if it contains chocolate chips, because the chocolate can get quite hot.
I love this method because you can bake a batch once and have a warm, homemade muffin ready whenever you want one!

New to Freshly Milled Flour?
One of my favorite ways to bake from scratch is with freshly milled flour! Milling wheat berries at home gives you fresh flour for everything from muffins and breads to pancakes and homemade pasta. I used freshly milled soft white wheat for these pumpkin oat muffins, and it’s a wonderful choice for tender, everyday baked goods. A deeper flavor profile and better nutrition is a win win!
If you’re curious about milling your own flour at home, a NutriMill grain mill is a great place to start! I’ll link the one I recommend below so you can explore whether freshly milled flour is right for your kitchen.

Frequently Asked Questions
Can I use regular sugar instead of monk fruit sweetener?
Yes! You can substitute granulated sugar or coconut sugar. I used ½ cup of monk fruit sweetener, so if you’re using a different product, check whether it measures cup-for-cup like sugar. The sweetness and final texture can vary slightly depending on the sweetener.
Can I make pumpkin oat muffins with chocolate chips?
Absolutely! Fold about ½ cup of dark chocolate chips into the batter before filling the muffin tin. You can use white chocolate chips instead or leave the chocolate out entirely.
How do I keep pumpkin muffins moist?
Pumpkin puree and unsweetened applesauce contribute moisture to these muffins. Measure the flour accurately, avoid adding extra flour, and stir the batter only until the ingredients are combined. Overmixing can make muffins tougher rather than tender.
Can I use freshly milled flour for pumpkin muffins?
Yes! I used freshly milled soft white wheat flour in this recipe. It works well for tender baked goods, although freshly milled flour can absorb liquid differently from store-bought flour. For the most consistent results, measure carefully and use the flour amount specified in the recipe.
Can I use quick oats instead of old-fashioned rolled oats?
Old-fashioned rolled oats are my preference because they provide a little more texture. Quick oats may work, but they can absorb moisture differently and produce a softer texture. I recommend starting with old-fashioned rolled oats for this recipe.
Can I make pumpkin oat muffins without chocolate chips?
Of course! The chocolate chips are an optional add-in, not a requirement. The muffins are delicious with just pumpkin, oats, and warm spices. You can also substitute nuts or pumpkin seeds if you’d like a different texture.
Can you freeze pumpkin muffins?
Yes! Allow them to cool completely, then package them in a freezer-safe bag or airtight container. For the best quality, enjoy them within about 3 months. You can thaw them at room temperature or warm an individual muffin in the microwave.
How long do homemade pumpkin muffins last?
Stored in an airtight container at room temperature, these muffins are best enjoyed within about 2 days. If you need to keep them longer, refrigerate them or freeze them. Freezing is my preferred option for maintaining a supply of homemade muffins without letting the extras go to waste.

In Closing
If you love pumpkin as much as I do, I hope these pumpkin oat muffins find their way into your fall baking rotation! Whether you enjoy them plain, with a handful of dark chocolate chips, or warm with cinnamon sugar honey butter, they’re a lovely way to bring a little homemade goodness into your day.
If you make them, I’d love to hear how you customized yours! Happy baking my friend!
XO, Bri
Let’s Stay Connected!
I’d love to stay connected with you! Follow along for more from-scratch recipes, seasonal inspiration, cozy home projects, and little glimpses of life here at Our Manor On Main. You can find me on the platforms below, and I’d love to have you join me there!




