With cream cheese filling to make this pumpkin muffin recipe fancy even though it’s super easy, and applesauce for moisture and reduced sugar, you can’t get any better than this. These soaked pumpkin muffins are healthy enough to eat for breakfast!
Do you have any favorite holiday dishes or recipes?
Mine is, hands down, my grandma’s pumpkin roll. I tweaked her recipe a bit to make it a tad healthier, but every time I take a bite of this dessert, I’m transported back to her kitchen table in Arkansas.
That’s why I decided to transform my favorite childhood dessert into muffin form. I mean, what could be better than a pumpkin muffin recipe with cream cheese filling!?
Reduced Sugar For Healthy Muffins
With some pumpkin muffin recipes calling for up to 3 cups (yes, 3 cups!) of white and brown sugars, we need an easy way to make them healthier.
This particular recipe has just 1 cup of unrefined sugar for the whole batch. But I’m adding my secret ingredient for making muffins healthier and tastier: applesauce!
The applesauce adds sweetness and moisture to the muffins, ensuring perfect results! Plus, it’s also fall-themed.
And instead of refined sugar, we’re using Rapadura or Sucanat which retain more minerals (you could also use coconut sugar).
This is actually what I do to all my muffin recipes to make them healthier (including these awesome pumpkin chocolate chip muffins). Add applesauce and reduce sugar.
Works every time, and they’re always super moist!
My family can’t detect the healthy tweaks one bit. My husband actually said these soaked pumpkin muffins are now his favorite baked item I’ve made in the past 12 years of our marriage!
Why Soaking Is An Important Step
Another important step to make muffins as healthy as possible is soaking.
What is soaking and why soak?
Grains and beans (and all seeds, including nuts and seeds) have anti-nutrients like phytic acid and enzyme inhibitors that can interfere with digestion and lead to mineral deficiencies. When you soak with an acid medium, the anti-nutrients are neutralized during the soaking period and result in a more digestible and nutritious dish. — from #AskWardee 007
Soaking also helps break down the more difficult-to-digest proteins in grain, such as gluten. Baking then deactivates the enzyme inhibitors.
So, if you want your muffins to be as healthy as possible, always soak your flour in an acidic medium first! This is very simple to do.
Just mix your flour, milk, and raw apple cider vinegar together in a large bowl, cover, and allow to soak overnight.
How To Make Soaked Pumpkin Muffins With Cream Cheese Filling
The next day, all you have to do is mix up the wet ingredients and baking powders/spices and add them to the soaked flour mixture.
Confession: it is definitely more difficult to mix the batter together thoroughly when your flour is pre-soaked. It takes more elbow grease, for sure, because the flour mixture will be quite gummy.
Yet… it only adds a couple additional minutes of mixing time. And you can work on your muscles while you’re at it! 😉
You got this! Make sure you use a good quality whisk.
If you’re blessed enough to own a stand mixer, this part is no problem at all. Let the mixer do all the work for you.
To spice up these muffins, I’m using an organic pumpkin pie spice blend. But if you don’t have any, here’s an easy 5 minute tutorial for how to make pumpkin pie spice in any amount you choose.
Make sure to fill your muffin tins almost all the way to the top with batter. Since they’re soaked, they don’t rise quite as high as a conventional muffin.
I like using paper liners for easy cleanup of the muffin pans. You could also try making mini muffins with this recipe — just reduce the baking time.
Once the muffin batter is prepped, you’re on to the fun part: cream cheese filling!
Tips For Perfect Cream Cheese Frosting Or Filling
One thing I love about these soaked pumpkin muffins is that they look so fancy and impressive with the cream cheese filling… even though it’s extremely easy to do!
The filling makes them sooooo rich and decadent.
First, let your cream cheese sit out at room temperature for a couple hours before baking to soften it.
While many cream cheese frosting recipes call for lots of refined or powdered sugar, we use maple syrup and vanilla extract to give it just the right amount of sweetness.
Whisk it with an electric mixer and add it to a piping bag or gallon Ziploc bag to fill the muffins. Simply insert the tip of the piping bag into the muffin and squeeze out some filling.
Another baking tip: With most muffin recipes, you use a toothpick inserted into the center of the muffin and see if it comes out clean to determine doneness.
With these, since the cream cheese filling is in the center, you’ll need to insert the toothpick slightly off center to test the cake-y part of the muffin.
Now get baking! Your friends and family will be SO impressed with these muffins at your next fall gathering.
Soaked Pumpkin Cream Cheese Muffins
With cream cheese filling to make this pumpkin muffin recipe fancy even though it's super easy, and applesauce for moisture and reduced sugar, you can't get any better than this. These soaked pumpkin muffins are healthy enough to eat for breakfast!
For the pumpkin muffins:
- 2 cups whole wheat pastry flour or all-purpose
- 1 cup raw milk
- 1 tablespoon raw apple cider vinegar
- 2 organic and/or pastured eggs
- 1 15-ounce can pumpkin puree
- 1 cup applesauce unsweetened
- 1/2 cup coconut oil melted
- 1 cup Rapadura or Sucanat or coconut sugar
- 2 teaspoons baking soda
- 1 teaspoon baking powder
- 1 tablespoon pumpkin pie spice
- 1 teaspoon sea salt
For the cream cheese filling:
- 8 ounces cream cheese or Neufchâtel cheese (softened)
- 1/4 cup maple syrup
- 1 teaspoon vanilla extract
Mix together flour, milk, and raw apple cider vinegar in a large bowl.
Cover and let soak overnight, up to 24 hours.
Preheat oven to 350 degrees Fahrenheit.
In a separate medium-sized bowl, whisk together eggs, pumpkin, applesauce, sweetener, baking soda, spices, and salt. Slowly add melted coconut oil to mixture, whisking in slowly.
Add pumpkin mixture to the soaked flour mixture.
Mix until smooth. It may take a little time and elbow grease to make sure everything is incorporated thoroughly. This is simply the nature of soaked muffins. If you have one, use a stand mixer.
Combine cream cheese, maple syrup, and vanilla extract in a small bowl.
Beat together until smooth with an electric hand mixer.
Transfer to a piping bag or gallon Ziploc bag, seal, and cut a hole in the tip.
Fill a muffin tin with paper liners.
Fill each muffin cup almost to the top with muffin batter.
In the center of each muffin cup, insert the piping bag and fill with cream cheese filling. Make sure some filling is showing on top of each muffin.
Bake for 20 to 25 minutes. Check them a minute or two early to check for doneness – don’t overcook. Test the cakey part of the muffin with a toothpick until it comes out almost clean.
Allow to cool for several minutes before enjoying.
Want some other ways to use pumpkin puree?
Some stores don’t carry pumpkin puree year-round, so I usually stock up in the fall and I can bake my favorite goodies whenever I want!
Pumpkin muffins in the summer? You bet!
Here are some other ways to use pumpkin puree:
- Instant Pot Grain-Free Pumpkin Cheesecake
- Sprouted Apple Pumpkin Breakfast Cookies
- Sprouted Pumpkin Spice Coffee Cake
- Sourdough Pumpkin Bread
- Spiced Pumpkin Chocolate-Chip Bundt Bread
- Cultured Pumpkin Pie Overnight Oats
- Pumpkin Pie Panna Cotta
- Sprouted Spelt Pumpkin Roll With Cream Cheese Filling
- Instant Pot Pumpkin Pudding (allergy-friendly!)
- Paleo Sugar Cookies With Pumpkin Glaze (easy fall gluten-free dessert!)
- 32 THM:S & Low-Carb Pumpkin Recipes (Dinner, Drinks, & Dessert!)
I hope you love this pumpkin muffin recipe as much as my family does! What is your best cake or cupcake or muffin recipe? Are you a pumpkin fan?
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Good morning! Can you use all-purpose gluten free flour in this recipe? How does it respond to “soaking”?
Mary Harp says
You should be able to, but I haven’t tried it personally. Let us know how it goes!
Marsha Whitt says
I used GF flour – they turned out great!
Sheryl Edwards says
These are fantastic!
Is there anything that could be substituted for the pumpkin purée to make different flavors?
Mary Harp says
Sheryl, you might be able to but I haven’t tried it! An apple muffin might be nice? If you use apple sauce the dough might be a bit wetter so you may need to reduce other liquid.
Can I sub maple syrup for the sugar? Would I just reduce liquid elsewhere?
Mary Harp says
You could try it, maybe eliminate the applesauce?
Can I substitute nut milk for raw milk and Himalayan salt for sea salt?
Mary Harp says
Yes, those substitutions should work fine!
Sheryl Edwards says
Can you use mashed bananas instead of pumpkin?
Marsha Whitt says
Thank you so much for this recipe! My substitutes:
All purpose gluten free flour,
2 ripe bananas in place of applesauce,
1/2 cup sugar plus a few shakes of Pyure pure stevia.
I mixed the soaked flour with half the wet ingredients in my food processor – easier then to stir in the rest.
They are fantastic, so moist, comforting, and satisfying with coffee! They taste a lot more like a pumpkin roll when they’re cool. I love them both ways.