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    Home » Recipes » Desserts

    Pumpkin Cheesecake Muffins

    Published: Nov 24, 2021 · Updated: Nov 24, 2021 by Natalie · 58 Comments

    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!

    Jump to:
    • Why do you need to make this?
    • Ingredients used
    • How to make Pumpkin Cheescake Muffins
    • Substitutions
    • Tips for storing
    • Recipe tips
    • Recipe variations
    • 📖 Recipe
    • More recipes to try
    • 💬 Comments
    Healthy Pumpkin Cheesecake Muffins

    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! 
    Fragrant, soft and lusciously sweet, Pumpkin Cheesecake Muffins made with all HEALTHY ingredients, refined sugar-free are the best thing this Fall. Flavored with real pumpkin and warm spices, filled with a cream cheese surprise it's a dessert that will make you wish pumpkin season last all year long. #pumpkin #fall #muffin #healthy #wholegrain #skinny #lowsugar #lowfat #easy #kidsfriendly #school #breakfast #dessert | natalieshealth.com

    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.
    Fragrant, soft and lusciously sweet, Pumpkin Cheesecake Muffins made with all HEALTHY ingredients, refined sugar-free are the best thing this Fall. Flavored with real pumpkin and warm spices, filled with a cream cheese surprise it's a dessert that will make you wish pumpkin season last all year long. #pumpkin #fall #muffin #healthy #wholegrain #skinny #lowsugar #lowfat #easy #kidsfriendly #school #breakfast #dessert | natalieshealth.com

    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. 
    Pumpkin Cheesecake Muffins

    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.
    Fragrant, soft and lusciously sweet, Pumpkin Cheesecake Muffins made with all HEALTHY ingredients, refined sugar-free are the best thing this Fall. Flavored with real pumpkin and warm spices, filled with a cream cheese surprise it's a dessert that will make you wish pumpkin season last all year long. #pumpkin #fall #muffin #healthy #wholegrain #skinny #lowsugar #lowfat #easy #kidsfriendly #school #breakfast #dessert | natalieshealth.com

    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.
    Fragrant, soft and lusciously sweet, Pumpkin Cheesecake Muffins made with all HEALTHY ingredients, refined sugar-free are the best thing this Fall. Flavored with real pumpkin and warm spices, filled with a cream cheese surprise it's a dessert that will make you wish pumpkin season last all year long. #pumpkin #fall #muffin #healthy #wholegrain #skinny #lowsugar #lowfat #easy #kidsfriendly #school #breakfast #dessert | natalieshealth.com

    📖 Recipe

    Healthy Pumpkin Cheesecake Muffins

    Pumpkin Cheesecake Muffins

    By Natalie
    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.
    5 from 39 votes
    Print Recipe Pin Recipe
    Prep Time 10 mins
    Cook Time 20 mins
    Total Time 30 mins
    Course Dessert
    Cuisine American, International
    Servings 12 muffins
    Calories 243 kcal

    Equipment

    • Measuring cups
    • Mixing bowls
    • Flexible silicone spatula
    • Whisk
    • 12-cup muffin tin
    • Muffin liners

    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.
    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.
    As a measure, I used US cup (240ml). See "Recipe tips" for more recipe info.

    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
    Keyword pumpkin cheescake muffins, pumpkin cream cheese muffins, pumpkin muffins with cream cheese filling
    Tried this recipe?Don’t forget to rate it and leave the comment. I would love to hear what you think.
    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.

    More recipes to try

    • Pumpkin Bars with Cream Cheese Frosting
    • Pumpkin Loaf Cake
    • Pumpkin Chocolate Chip Bread
    • Pumpkin Roll Cake
    « Pumpkin Baked Oatmeal
    What's in season: DECEMBER »

    About Natalie

    Natalie Knezic is a writer, recipe developer, and creator of Natalie's Health. She's also a certified nutrition coach and weight loss specialist. She actively coaches, creates recipes and writes about a healthy lifestyle. Her recipes and articles have been featured in many popular media outlets, like Shape, Greatist, Pure Wow, Mashed, The Huffington Post, ELLE Magazine, and many more.

    Reader Interactions

    Comments

    1. Morgan says

      September 15, 2017 at 8:20 pm

      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

      Reply
      • Natalie says

        September 18, 2017 at 8:17 am

        Oh you must try these then ;)

    2. Deborah @ Confessions of a mother runner says

      September 15, 2017 at 7:48 pm

      I am almost ready for all things pumpkin! These look delicious

      Reply
      • Natalie says

        September 18, 2017 at 8:17 am

        Thanks my friend! :)

    3. Rachel says

      September 15, 2017 at 7:32 pm

      Yum! I make a pumpkin cheesecake with a caramel swirl for Thanksgiving. But MUFFINS sound even better!!!

      Reply
      • Natalie says

        September 18, 2017 at 8:19 am

        Thanks Rachel :) Pumpkin cheesecake with caramel swirl?! Now THAT sounds amazing. :D

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    Hi, I’m Natalie, a writer, recipe developer, and certified nutrition coach. I love creating recipes that taste delicious using wholesome ingredients that contribute to our health. On my blog, you'll find many such recipes and tips on how to live a healthier, happier life. I'm so glad you are here! Find out more about me.

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