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Pumpkin Recipes

Pumpkin Cheesecake Muffins

Pumpkin cheesecake muffins are a pumpkin swirled cream cheese muffin with a spiced streusel crumb and pumpkin seed topping. They’re super moist and fluffy and taste like everything we love about the season!

pumpkin cream cheese muffins with crumb topping

Extra moist and fluffy with a spiced streusel topping, these pumpkin cheesecake muffins are truly the best muffin for fall! They pop out of the pan with a perfectly fluffy muffin top just like you would expect from a pumpkin muffin from a bakery, and will make your whole house smell amazing while they bake.

Typically on Once Upon a Pumpkin I make healthier versions of pumpkin recipes. I strive to bake up fun pumpkin treats with a little less sugar, perhaps made gluten free and or with just a few simple ingredients.

The thing about the fall is that it brings about a feeling of nostalgia that we look forward to all year. That comfort and coziness that comes from the smell of cinnamon, crisp air and golden hues. As a dietitian, I think I do a pretty good job of bringing that into my healthier pumpkin recipes, but sometimes you just can’t beat the real thing made with traditional ingredients.

That is the balance I preach through this site and on my Instagram page — nutrition that is about mindful choices that honor how you feel, are enjoyable and allow you to enjoy your life (and live your best fall life!).

These bakery-style pumpkin muffins will hopefully remind you of your love of all things fall, baking with your mom or grandma and taking in all the scents and flavors of the season.

This pumpkin recipe uses an entire can of pumpkin puree, and lots of fall spices that will have your whole house smelling amazing. The silky smooth cream cheese layer in between layers of fluffy pumpkin muffin is my favorite part!

So get out your cans of pumpkin, light a fall candle and let’s make these irresistible pumpkin cream cheese muffins!

Ingredients for Pumpkin Cheesecake Muffins with Streusel Topping

  • Organic All-purpose Flour or White Whole-Wheat Flour
  • Pumpkin Pureethis muffin recipes uses an entire can of pumpkin puree! Make sure it’s 100% pure pumpkin and not pumpkin pie mix.
  • Coconut Oil
  • Eggs + egg yolk
  • Light Brown Sugar
  • Pumpkin Spice
  • Cinnamon
  • Baking Soda
  • Baking Powder
  • Cream Cheese
  • Butter
  • Pumpkin Seeds

Equipment / utensils

  • mixing bowls
  • whisk
  • wooden spoon
  • muffin pan
  • muffin liners

Tips for Making the Best Pumpkin Muffins

  1. Measure the flour correctly. Too much flour can definitely impact how these muffins turn out. Use a scoop to scoop flour into a measuring cup (don’t pack it in!) to ensure you don’t have too much.
  2. Don’t over mix the batter. Muffin batter shouldn’t be super smooth. You want there to be bumps. Just as soon as you don’t see any major streaks of flour, stop mixing.
  3. Make sure the baking soda and baking powder are fresh. This is a sneaky little thing I think a lot of us don’t think about. If your baking soda or baking powder has been sitting untouched since last fall when you baked something, this could be impacting your baked goods negatively. Check the date on the label!
pumpkin cream cheese muffins with crumb topping

Pumpkin Cheesecake Muffins

Pumpkin cheesecake muffins are super fluffy, spiced just right and taste like everything we love about fall. Enjoy one with a cup of coffee for all the fall feels!
Prep Time 15 mins
Cook Time 25 mins
Servings 12 muffins


  • 2 mixing bowls
  • 1 Whisk
  • 1 wooden spoon
  • 1 muffin pan
  • 12 muffin liners


For the pumpkin muffin batter

  • 2 cups organic all-purpose flour
  • 2 tsp. baking powder
  • 1 tsp. baking soda
  • 1/4 tsp salt
  • 2 tsp. cinnamon
  • 2 tsp. pumpkin pie spice
  • 1 15 oz. can pumpkin puree
  • 2 eggs at room temperature
  • 1/2 cup coconut oil melted
  • 1 cup light brown sugar
  • 1 tsp vanilla extract

For the Streusel Topping

  • 1/3 cup brown sugar
  • 3 tbsp butter melted
  • 2 tsp. pumpkin spice
  • 1/4 tsp. salt
  • 1/2 cup all-purpose flour

For the Cream Cheese Layer

  • 8 oz cream cheese softened
  • 1 egg yolk
  • 1 tsp. vanilla extract


  • Preheat the oven to 400 degrees F and line a muffin pan with muffin liners, lightly spraying the inside with baking spray or oil so that that the muffins don't stick to the liners.
  • Get out the cream cheese and butter to soften and bring to room temperature.
  • In a medium sized mixing bowl whisk together the flour, baking powder, baking soda, cinnamon, pumpkin spice and salt. Set aside.
  • In another medium sized bowl, whisk together the pumpkin puree, eggs, coconut oil, brown sugar and vanilla until smooth.
  • Add the dry ingredients to the wet and combine using a wooden spoon careful not to over mix.
  • Make the cream cheese mixture by beating together softened cream cheese, egg yolk and vanilla extract.
  • Use an ice cream scoop to scoop the muffin batter into the muffin liner so that they're about 1/3 of the way filled. Spoon about 1 tablespoon of the cream cheese on top and then cover with remaining pumpkin batter (it's ok if the batter doesn't completely cover the cream cheese batter).
  • Make the streusel topping by combining the brown sugar, pumpkin pie spice, salt and and flour. Add melted butter and use a fork to mix it around into crumbs — it shouldn't be a super fine consistency.
  • Sprinkle the crumb topping and pumpkin seeds if desired over each. Bake for 23-25 minutes (checking at 23 minutes). Let cool and enjoy!

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Pumpkin Cheesecake Muffins with Spiced Streusel Topping and Pumpkin Seeds
Pumpkin Recipes

Pumpkin Gingerbread Muffins with Lemon Glaze

Pumpkin gingerbread muffins with lemon glaze are gluten free, dairy free, and naturally sweetened — the perfect muffins for the holiday season! They are packed with pumpkin, warm spices and molasses for that gingerbread taste!

fluffy, moist and delicious gluten and dairy free pumpkin gingerbread muffins with fresh orange zest
In this batch of muffins, I used regular molasses, not blackstrap which is why they are lighter in color.

If you’re like me and not quite ready to give up on pumpkin after Halloween or Thanksgiving, whip up a batch of these healthy pumpkin gingerbread muffins made with simple ingredients in December! Molasses and ginger give them extra holiday flavor and that classic gingerbread taste. I say pumpkin season is truly year-round!

Made gluten and dairy free with a blend of almond and oat flour, these healthy pumpkin gingerbread muffins will hit the spot alongside a cup of coffee on a chilly December morning. The citrus glaze is totally optional, but it definitely adds a little extra flavor and bright sweetness.

Pumpkin Gingerbread Muffins

Pumpkin puree, pumpkin spice, ginger and molasses come together for a perfectly spiced muffin that marries the flavors of fall and winter! The blend of almond and oat flour in this recipe give the muffins an extra fluffy and soft texture that I know you’ll love as much as I do!

One tip to keep in mind when you’re baking any type of muffins is to not over mix the batter. The batter should be mixed together just so and you should still see some lumps. At that point you can start portioning out the batter into the individual muffin tins.

best pumpkin gingerbread muffins

Nutrition Benefits of Pumpkin Puree

Pumpkin puree is a great source of a lot of vitamins and minerals which is one of the many reasons I love cooking and baking with it all fall long! It’s super versatile, adding flavor and texture to both sweet and savory foods — not many other fruits and vegetables can say the same.

Maybe you’ve noticed that a lot of gingerbread flavored treats contain molasses, but what is molasses and is it good for you? Let’s find out!

healthy gingerbread muffins

What is Molasses and is it Healthy?

Blackstrap molasses is a byproduct of sugar cane’s refining process. Sugar cane is mashed to create juice, and then boiled once to create cane syrup. A second boiling creates molasses.

Blackstrap molasses has the lowest sugar content of any sugar cane product and is actually packed with vitamins and minerals like iron, calcium, magnesium, B6 and selenium. It’s also digested slower than other sweeteners, which is good for blood sugar balance. Known for giving gingerbread its distinctive taste, you can use it in other ways too like a glaze for chicken!

almond flour gingerbread muffins

Ingredients for almond flour gingerbread muffins

Here’s everything you will need to make these pumpkin gingerbread muffins with lemon glaze!

  • blanched almond flour
  • oat flour (gluten free if preferred)whole-wheat pastry flour can be substituted for oat flour. Note, whole-wheat pastry flour is not gluten free.
  • blackstrap molassesmolasses is what gives these muffins that gingerbread flavor. You can definitely use regular molasses vs. blackstrap. Your muffins will come out lighter in color when using regular molasses.
  • pumpkin pureeas with any of my pumpkin recipes, be sure to use pumpkin puree and not pumpkin pie filling! I love using Libby’s 100% Pure Pumpkin in all of my pumpkin recipes.
  • maple syrup
  • unsweetened almond milk or other milk of choice
  • pumpkin pie spice
  • lemon juice
  • lemon zest or orange zest
  • coconut oil
  • baking soda
  • confectioners sugar

equipment / utensils needed:

How to Make The Glaze

Making the lemony glaze for these gluten free gingerbread muffins is super easy! All you need to do is mix together the confectioners sugar, maple syrup, lemon juice, and vanilla extract.

You want the consistency to be thin enough to drizzle on top of each muffin. If your icing is too thick add a little more almond milk, if it’s too thin, add more confectioners sugar. I love grating fresh lemon or orange zest into the glaze as well to add more fresh, bright flavor.

The rind of citrus fruits also contains vitamin C so you can feel good knowing you’re getting a little more of that too!

almond flour gingerbread muffins

Pumpkin Gingerbread Muffins with Lemon Glaze

Maggie Michalczyk, RDN
Extra flavorful and fluffy, you’ll love this festive gingerbread spin on a classic pumpkin muffin! Made gluten free with simple ingredients, these muffins are the perfect healthier treat to bake up in December. 
Prep Time 10 mins
Cook Time 22 mins
Servings 12 muffins


For the muffins: 

  • 1 cup oat flour
  • 1 cup blanched almond flour
  • 2 tsp. pumpkin pie spice
  • 1 tsp. cinnamon
  • 1 tsp. ground ginger
  • 1/4 tsp. nutmeg
  • 1/4 tsp. salt
  • 3/4 tsp. baking soda
  • 2 eggs lightly beaten
  • 1/3 cup pumpkin puree
  • 1/3 cup maple syrup
  • 2 tbsp. molasses
  • 1 tsp. vanilla extract
  • 1/2 cup unsweetened almond milk
  • 1 tsp. coconut oil
  • 1 tsp.fresh lemon juice

for the lemon glaze:

  • 1/2 cup confectioners sugar
  • 1 1/2 tsp. maple syrup
  • 2 tsp. lemon juice
  • fresh lemon or orange zest


  • Preheat oven to 350 degrees F. Line 12 muffin cups with liners and spray the inside of the liners with nonstick cooking spray so the muffins do not stick.
  • In a medium bowl, whisk together oat flour, almond flour, pumpkin pie spice, cinnamon, ginger, nutmeg, salt and baking soda.
  • In a separate large bowl, mix together eggs, pumpkin puree, maple syrup, molasses, vanilla extract, almond milk, coconut oil and lemon juice until smooth and well combined. Pour the wet ingredients into the dry ingredients and use a wooden spoon stir until just combined.
  • Divide batter evenly in each muffin tin. Bake for 20-22 minutes.
  • While the muffins are baking whisk together the ingredients for the lemon maple glaze. It should be thick enough to drizzle. If too thick, add a little more lemon juice or almond milk to thin it out. 
  • Remove muffins from the oven and let cool. Use a fork to drizzle icing on top of each. Top with extra pumpkin pie spice and fresh lemon or orange zest. Enjoy! 
Keyword pumpkin muffins; pumpkin gingerbread muffins; gingerbread muffins; gluten free pumpkin muffins

This recipe was originally posted in November of 2020 and updated in December 2021.

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gingerbread muffins with lemon glaze
Nutritious Treats

Healthy Whole-Grain Pumpkin Blueberry Muffins

Whole-grain blueberry pumpkin muffins are spiced just right, with blueberries in every bite! Made with simple ingredients, including canned pumpkin and fresh blueberries, they make for a nutritious breakfast or snack any time of year.

July is National Blueberry Month, but let’s be honest, the celebration should be all year-long because there are endless ways to incorporate blueberries for a delicious pop of flavor, nutrition, and boost of blue! If you’re following along on Instagram, then you know this week is #BLUEBERRYWEEK where I’m sharing different ways to incorporate blueberries in meals and snacks. 

A classic way to enjoy blueberries are in blueberry muffins. For this blueberry muffin recipe, I’m putting a pumpkin spin on it perfect for summer or fall!

Topped with a cinnamon crumb topping and packed with blueberries in every bite with hints of pumpkin and pumpkin spice, they’ll be your new favorite way to use blueberries.

I’m excited to partner with the U.S. Highbush Blueberry Council on this recipe that combines my love for all things pumpkin and blueberries! I always have a carton of blueberries in my fridge and a can of pumpkin in my pantry, so these muffins are truly the best of both worlds! 

whole wheat pumpkin blueberry muffins

Blueberry Nutrition 

one-cup serving of blueberries delivers crave-worthy flavor and beneficial vitamins and minerals, including four essential nutrients –  vitamin C, vitamin K, manganese, and fiber – and phytonutrients.  

Just one serving provides 16 percent of the daily recommended amount of vitamin C. As you may know, vitamin C is an antioxidant that supports a healthy immune system, helps protect cells from damage caused by free radicals and helps the body to absorb iron from plant-based foods. The body also needs vitamin C to make collagen. 

A growing body of scientific evidence demonstrates that blueberries can be part of eating patterns to improve cardiovascular health and support brain health, especially as part of an overall healthy lifestyle. This is super exciting because blueberries are so easy to incorporate into the diet. 

Besides washing, they require zero preparation, which makes them an ideal snack, especially when you’re pressed for time. Simply rinse and go! Here are a few ways I like incorporating a boost of blue into my diet daily: 

  • Sprinkling on top of oatmeal & yogurt
  • Simply grabbing a handful right out of the fridge!
  • Making a homemade trail mix with dried blueberries, chocolate chips and walnuts
  • Adding frozen blueberries to a smoothie to make it extra thick and creamy
  • Adding a handful to a grain bowl with quinoa and greens

Check out this post to learn more about the nutrition benefits of blueberries and get inspired so you can incorporate them into snacks and meals! 

best pumpkin blueberry muffins

Frozen Blueberries 

Are frozen blueberries just as nutritious? Yes! Frozen blueberries are a convenient and cost-effective way to help you eat nutritiously. They’re frozen at the peak of freshness, locking in their healthy goodness. And just like fresh blueberries, frozen blueberries are a good source of fiber. Having frozen blueberries on hand is a huge time-saver since you can buy them well in advance of using them. 

Ingredients for whole-grain pumpkin blueberry muffins 

  • Blueberries – You might be wondering; can you use frozen blueberries in baking? The answer is yes. You can use fresh or frozen in this recipe!
  • Pumpkin puree Pumpkin adds a beautiful texture and flavor to these muffins. Pumpkin puree can also act as a replacement for eggs in baked goods. 
  • Whole-wheat pastry flour
  • Eggs
  • Coconut oil
  • Light brown sugar or coconut sugar
  • Non-dairy milk
  • Vanilla extract
  • Pumpkin pie spice
  • Nutmeg
  • Baking powder 
  • Salt

How to Make Pumpkin Blueberry Bread with this Muffin Batter

You can easily turn these muffins into a pumpkin blueberry loaf simply by lowering the oven temperature to 350 degrees Fahrenheit and increasing the cook time to 50-55 minutes. I recommend using an 8X5 loaf pan. 

whole wheat pumpkin blueberry muffins

Healthy Whole-Grain Pumpkin Blueberry Muffins

Maggie Michalczyk, RDN
Pumpkin blueberry muffins will be your new favorite spin on a pumpkin muffin! Pumpkin spiced just right with blueberries in every bite, they’re fluffy and fun for fall or summer!
Prep Time 10 mins
Cook Time 25 mins
Servings 12 muffins


  • for the muffin batter:
  • 2 cups + 1 tbsp. whole-wheat pastry flour
  • 2 tsp. pumpkin pie spice
  • ¼ tsp. nutmeg
  • 2 tsp. baking powder
  • ¼ tsp. salt
  • 2 eggs
  • 3/4 cup light brown sugar
  • ½ cup coconut oil melted
  • ¼ cup non-dairy milk
  • 1 tsp. vanilla extract
  • 1 cup pumpkin puree
  • 1 ¼ cup blueberries

For the crumb topping:

  • 1/4 cup whole-wheat pastry flour
  • 1/2 teaspoon pumpkin pie spice
  • Pinch of nutmeg
  • 1/4 cup packed brown sugar
  • 2 tbsp. butter melted


  • Preheat the oven to 375 degrees Fahrenheit and line a muffin tin with muffin liners. Spray the liners with cooking spray to prevent muffins from sticking.
  • In a medium bowl, whisk the eggs, brown sugar, coconut oil, milk, vanilla extract, and pumpkin puree.
  • In a separate bowl whisk the whole-wheat pastry flour, pumpkin pie spice, baking powder and salt.
  • Add the dry ingredients to the wet ingredients, and stir together with a wooden spoon, being careful not to over mix.
  • Coat blueberries with 1 tbsp. of flour to prevent them from sinking to the bottom of the batter and fold into mixture.
  • Make the crumb topping by combining the flour, pumpkin pie spice, nutmeg, and melted butter. Use your hands or a fork to mix until crumb pieces begin to form.
  • Use an ice cream scoop to divide the batter among the muffin tins and sprinkle crumb topping over each one.
  • Bake for approximately 25 minutes. A toothpick should come out clean with just a few crumbs attached to indicate doneness.
  • Enjoy once cooled and store covered in the fridge for maximum freshness!
Keyword pumpkin blueberry muffins; pumpkin muffins

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more pumpkin muffins recipes you’re sure to love:

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how to make pumpkin blueberry muffins
Pumpkin Muffins

Pumpkin Morning Glory Muffins

Pumpkin morning glory muffins are bursting with nutrition, texture and flavor and are made with pumpkin, apple, and zucchini!

They are the muffins you never knew you needed, with pumpkin, zucchini and apple all rolled into one delicious baked good! They’re perfect with a cup of coffee in the morning or slathered with almond butter as a snack!

These muffins are grain free and made with almond flour, eggs, pumpkin, zucchini, apple and sweetened with maple syrup. I often crave a baked good in the morning but don’t want something that is overly sugary or sweet. Luckily, these muffins are lightly sweetened and help me get more fruits in at breakfast!

pumpkin muffins with zucchini and apple

There are many renditions of morning glory muffins. Some with carrots, and raisins and some with walnuts and coconut. Those things can totally be added into this batter! I choose to keep this batch simple, but that didn’t stop me from drizzling almond butter all over them when they were still warm out of the oven!

The pumpkin seeds on top give these muffins a nice crunch. It may not be fall yet, but one bite of these muffins and you’ll be excited for more pumpkin goodies to come!

grain free pumpkin morning glory muffins

Pumpkin, zucchini and apples all contain vitamins, minerals and fiber that we need in our diet daily. All three fruits (yes, pumpkin and zucchini are technically fruits!) contain vitamin C, A and potassium. They are also all a good source of fiber, nutrient that most of us don’t get enough of on a daily basis!

delicious pumpkin morning glory muffins

If you love a good baked good with pumpkin, be sure to check out this recipe for gluten free pumpkin chickpea blondies and theses paleo pumpkin zucchini banana muffins!

Grab what you need for this recipe here:

Best Pumpkin Morning Glory Muffins

Grain Free Pumpkin Morning Glory Muffins

Maggie Michalczyk, RDN
Made with delicious and nutritious ingredients you’ll want to start every week with a warm batch of these pumpkin morning glory muffins! 
Prep Time 10 mins
Cook Time 30 mins
Servings 11 muffins


  • 2 cups almond flour
  • 2 eggs
  • 1/4 cup maple syrup*
  • 2/3 cup pumpkin puree
  • 1 cup shredded zucchini squeezed of excess moisture with a paper towel (really squeeze!)
  • 1 large apple I originally used a honey crisp washed and cut into thin strips, and then diced (to still get little apple pieces)
  • 2 tsp. pumpkin pie spice
  • 2 tsp. fresh ginger pealed and grated
  • 1 tsp. vanilla extract
  • 1 tsp. baking powder
  • 1/4 tsp. baking soda
  • 1/2 tsp. salt
  • pinch of nutmeg
  • 2 tbsp. pumpkin seeds pepitas for sprinkling on top
  • optional mix-ins: walnuts pecans, chocolate chips, dried cranberries, unsweetened coconut flakes


  • 1. Preheat the oven to 375°F. Lightly grease a 12-cup muffin tin, or line it with papers and spray the insides of the papers.
  • 2. In a large bowl, whisk together the flour, pumpkin pie spice, baking soda, baking powder, and salt.
  • 3. In a separate bowl, combine the eggs, pumpkin puree, maple syrup, zucchini, apples, ginger, and vanilla until combined.
  • 4. Add the dry ingredients to the wet ingredients and mix until just combined — don’t over mix!
  • 5. Use an ice cream scoop or a small measuring cup to scoop batter into muffin tins. Sprinkle pumpkin seeds on top. 
  • 6. Bake for 28-30 minutes. Remove from oven, use a knife to loosen them from the muffin pan if needed. Let cool and enjoy! 
  • 7. Store in the fridge for up to 1 week in an airtight container. 


* Can substitute coconut sugar or brown sugar if needed. 



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