These Pumpkin Cheesecake Muffins are sweet and full of seasonal flavors. Packed with real pumpkin and cream cheese filling, it's an extra delicious dessert perfect for cozy Fall afternoons. Bonus: they only take 30 minutes!
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There's no better way to celebrate beautiful Fall than with a cup of Pumpkin Latte and deliciously sweet Pumpkin Cheesecake Muffins.
These pumpkin cream cheese muffins are sweet and delicate, super moist, and full of warm seasonal spices. Also filled with tangy cream cheese surprise. Such a delicious treat to have on afternoons.
These pumpkin cheesecake muffins are a great addition to your holiday table as well. Everyone will love them. You might want to make a double batch because these pumpkin muffins tend to disappear fast!
Why do you need to make this?
- Pumpkin Cheescake Muffins are delicious, filled with real pumpkin and seasonal spices.
- They are easy to make, in one-bowl, with simple pantry ingredients.
- They are packed with fibers from wholegrain flour.
- They are made without unhealthy processed sugars.
- A great way to add pumpkin to sweet treats. Pumpkins are packed full of nutrients and antioxidans!
Ingredients used
This pumpkin muffins recipe is very simple. You will need only basic pantry ingredients:
- Whole grain flour. It's a healthier, more nutritious option than all-purpose flour. I use it for all my baking. Whole grain flour is packed with fibers and makes everything more nutritious. In this recipe, I used whole grain Spelt flour, but you can use any whole grain flour.
- Sweetener. I used maple syrup, but you can use honey here. See "Recipe tips" for more suggestions.
- Pumpkin puree. Pumpkin puree is sweet and flavorful but also loaded with nutrients. It gave muffins extra sweetness and flavor.
- Pumpkin spice. I love the homemade Pumpkin Pie Spice blend. It features super spice Ceylon cinnamon known for its anti-inflammatory properties. (1).
Other pantry ingredients you’ll need:
- Eggs. Free-range, pasture-raised is the best.
- Vanilla extract.
- Baking soda.
- Pinch of salt.
- Extra virgin coconut oil.
- Muscovado sugar. For a little extra depth of flavor.
- Cream cheese. For the filling.
How to make Pumpkin Cheescake Muffins
This pumpkin muffins recipe is quite easy. Preparation takes no more than 10 minutes. The rest is baking time, and for that, you will only need patience.
Equipment used
- Measuring cups.
- Mixing bowls.
- 12-cup muffin tin.
- Muffin liners.
Step by step instructions
- Step 1: Prepare the ingredients.
- Preheat the oven at 190°C/375°F.
- Place muffin liners in a muffin tin. Set aside.
- Melt coconut oil and let it cool for a few minutes a room temperature.
- Measure all the ingredients using measuring cups.
- Step 2: Make the filling.
- In a small bowl, whisk together cream cheese with egg yolk and vanilla extract. Set aside.
- Step 3: Mix dry ingredients.
- In a medium bowl, mix together flour, spices, salt, and soda.
- Use the spoon or a whisk. Set aside.
- Step 4: Mix wet ingredients.
- In a separate large bowl whisk the eggs with coconut oil, pumpkin puree, maple syrup, and vanilla extract.
- Mix everything using the whisk until you get a nice sticky mixture.
- Step 5: Assemble and bake.
- Add dry ingredients into wet ingredients. Stir the batter using a spatula.
- Gently fold muscovado sugar into the batter. Don't overmix the batter.
- Spoon the batter into muffin liners, filling them ¾ full.
- Add a teaspoon of cream cheese filling and swirl it with a toothpick.
- Pop the muffins into the preheated oven and bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean.
Substitutions
- You can substitute Spelt flour with any whole grain flour. Or use plain/all-purpose flour if you prefer. Substitute at a 1:1 ratio.
- You can substitute maple syrup with honey. See "Recipe tips" for more suggestions.
- You can substitute coconut oil with avocado oil or grass-fed butter.
- You can substitute muscovado sugar with brown sugar or coconut sugar.
- For 1 teaspoon pumpkin pie spice, substitute: ¾ teaspoon cinnamon + ¼ teaspoon ginger + a dash of allspice, and nutmeg, with just a touch of cloves.
Tips for storing
- Counter: Once muffins are completely cooled, store them in an airtight container and keep them on the counter for up to 3 – 4 days.
- Refrigerator: Muffins will keep for up to a week in the refrigerator, in an airtight container.
- How to freeze? Place the muffins in a zip-lock bag. Keep in the freezer for up to 3 months. Thaw on room temperature.
- Muffins can be warmed in the microwave. Be careful not to overheat them.
Recipe tips
- When folding the batter, use the spatula and don't over-mix it. You need to have air bubbles in the batter. They make a lighter muffins.
- To check whether muffins are done, insert a skewer or toothpick into the center. If the toothpick comes out clean or with just a few crumbs on it, they are ready to come out of the oven.
- Make sure you use eggs at room temperature. Pull them out of the fridge before baking so they can rest for a bit. Or run the eggs under warm water to speed this process or set them in a bowl of warm water.
- If substituting coconut oil with salted butter, omit adding salt.
- Sweetener recommendation:
- You can use honey or maple syrup here. Make sure you use honey in liquid form.
- Date syrup or molasses are great options too. Note that they can make muffins darker in color.
- Use stevia or any low-carb sweetener.
- Make sure to use organic virgin coconut oil rather than refined versions.
Recipe variations
- Add in dried fruits: cranberries, raisins, sultanas.
- Add in chopped nuts: walnuts, pine nuts, hazelnuts, pecans.
- Make it protein-packed: You can replace ¼ cup of flour with 1 scoop of protein powder. I reccomend vanilla flavored. In that case you can omit adding vanilla extrat and you can reduce amount of sweetener.
- Make it gluten-free: Substitute whole-grain flour with any gluten-free flour.
📖 Recipe
Pumpkin Cheesecake Muffins
These Pumpkin Cheesecake Muffins are sweet and full of seasonal flavors. Packed with real pumpkin and cream cheese filling, it's an extra delicious dessert perfect for afternoons.
Equipment
- 12-cup muffin tin
Ingredients
For the muffins:
- 1 ¾ cups whole wheat flour
- 1 teaspoon pumpkin spice mix
- 1 teaspoon baking soda
- ½ teaspoon Himalayan salt
- 2 large eggs
- 1 cup pumpkin puree
- ½ cup extra virgin coconut oil melted and cooled
- ½ cup pure maple syrup
- 1 teaspoon vanilla extract
- 1 tablespoon muscovado sugar (optional)
For the filling:
- 1 cup cream cheese
- 1 egg yolk
- 1 teaspoon vanilla extract
Instructions
- Preheat the oven at 190°C/375°F. Place muffin liners in a muffin tin. Set aside.
- In a small bowl, whisk together cream cheese with egg yolk and vanilla extract. Set aside.
- In a medium bowl, mix together flour, spices, salt, and soda. Use the spoon or a whisk. Set aside.
- In a separate large bowl whisk the eggs with coconut oil, pumpkin puree, maple syrup, and vanilla extract. Mix everything using the whisk until you get a nice sticky mixture.
- Add dry ingredients into wet ingredients. Stir the batter using a spatula. Gently fold muscovado sugar into the batter. Don't overmix the batter.
- Spoon the batter into muffin liners, filling them ¾ full.
- Add a teaspoon of cream cheese filling and swirl it with a toothpick.
- Pop the muffins into the preheated oven and bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean.
Notes
Makes 12 muffins that serve 6-12 people. The suggested serving size is one muffin.
Substitutions
- You can substitute Spelt flour with any whole grain flour. Or use plain/all-purpose flour if you prefer. Substitute at a 1:1 ratio.
- You can substitute maple syrup with honey. See "Recipe tips" for more suggestions.
- You can substitute coconut oil with avocado oil or grass-fed butter.
- You can substitute muscovado sugar with brown sugar or coconut sugar.
- For 1 teaspoon pumpkin pie spice, substitute: ¾ teaspoon cinnamon + ¼ teaspoon ginger + a dash of allspice, and nutmeg, with just a touch of cloves.
- Counter: Once muffins are completely cooled, store them in an airtight container and keep them on the counter for up to 3 – 4 days.
- Refrigerator: Muffins will keep for up to a week in the refrigerator, in an airtight container.
- How to freeze? Place the muffins in a zip-lock bag. Keep in the freezer for up to 3 months. Thaw on room temperature.
- Muffins can be warmed in the microwave. Be careful not to overheat them.
Nutrition
Serving: 1muffin | Calories: 243kcal | Carbohydrates: 26g | Protein: 5g | Fat: 14g | Saturated Fat: 10g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 54mg | Sodium: 296mg | Potassium: 200mg | Fiber: 2g | Sugar: 11g | Vitamin A: 3351IU | Vitamin C: 1mg | Calcium: 64mg | Iron: 1mg
Tried this recipe?Pease leave a comment letting me know how you liked it. I love hearing from you!
DisclaimerThe nutritional information provided is approximate and is calculated using online tools. Information can vary depending on various factors, but I have endeavored to be as accurate as possible.
This post is originally published in September 2017. It's updated with new information and republished in November 2021. The recipe is changed slightly as I tested it more during that time.
Carol Borchardt says
Pumpkin and cheesecake are two of my most favorite things in life! I love that they're healthy-ish, too! Pinning this to make for a personal chef client; their kids will love them!
Christine says
These look SO delicious! Loving pumpkin everything right now. It's the best!! And love the cheesecake variation, too!
Marisa Franca @ All Our Way says
I can see why you chose to make the beautiful pumpkin cheesecake muffins instead of a soup. They look so moist and tasty. I'm in the mood for pumpkin spice -- I've yet to indulge this season. This recipe would be a great way to start.
Tina Lindquist says
This is super clever, I love pumpkin and am always trying to find ways to use it. This looks delicious, I can almost taste your photos:)
Carrie says
Oh my goodness if these muffin even taste half as good as they look my family will be in heaven! I am adding this to my baking list the weekend! Absolutely shared!
Marsha | Marsha's Baking Addiction says
These muffins sound absolutely wonderful! Just look how tall they are, too! <3 Happy Monday, Natalie! :)
Natalie says
Thank you Marsha. Happy new week to you too! :)
Ana SAV says
This looks amazing!! So glad I found your website!
Natalie says
Glad you like it Ana. Enjoy! :)
Tracy says
Oh wow! They sound and look delicious - your photos are stunning, too x
Natalie says
Thank you so much Tracy :) Glad you like it!
Jill Conyers says
I be the house smells so good while these are baking. All the pumpkin love!
Natalie says
Absolutely amazing! We couldn't wait to get them out of the oven :)
Esther says
Those look delicious! And seems like pumpkin snuck into my life the same way it snuck into yours! <3
Natalie says
Hehe thanks Esther! Lets this year's pumpkin season last LONG! ;)
Angela @marathonsandmotivation.com says
Yum! These sound like the perfect Fall treat. I have pinned this recipe to try :-)
Natalie says
Glad you like it Angela. Yes, these are perfect fall treat. We love it!
Trang says
These look scrumptious! I'm so ready for all things pumpkins :) especially muffins because I always crave something sweet with my morning coffee.
Natalie says
Heheh me too :) Muffins are so easy to make.
Tina says
This looks like such a good recipe. I love that there is no refined sugar in it. What a perfect treat for the fall.
Natalie says
Thanks Tina :) I'm glad you like the recipe!
Meliann says
I love pumpkin and I love cheesecake! This is a perfect combo for me! I will definitely try to make this soon! Thanks for sharing! :D :D :D
Natalie says
Pumpkin and cheesecake, it's my new fav combo ;) Thanks Meliann!
Maggie Unzueta says
Wow! These muffins look so good. I would love one with my morning coffee.
Natalie says
Thanks Maggie! Coffee + these muffins = perfect morning ;)
Jacqueline Meldrum says
Those looks heavenly and then you opened one up and they looked even better. Shared!
Natalie says
Thank you sooo much :)
Abbey Sharp says
These look AHHMAZING. I am definitely a pumpkin muffin fan, so I must try these out while fall is still on!
Natalie says
Enjoy Abbey! These are guilt free too ;)
Morgan says
These look amazing! Pumpkin bread is really the only way I like pumpkin, but I'd be more than willing to try out these muffins! Thanks for the recipe!
Morgan @ morganmabelle.com
Natalie says
Oh you must try these then ;)
Deborah @ Confessions of a mother runner says
I am almost ready for all things pumpkin! These look delicious
Natalie says
Thanks my friend! :)
Rachel says
Yum! I make a pumpkin cheesecake with a caramel swirl for Thanksgiving. But MUFFINS sound even better!!!
Natalie says
Thanks Rachel :) Pumpkin cheesecake with caramel swirl?! Now THAT sounds amazing. :D