Oh my gosh, you guys – these pumpkin cheesecake cupcakes are my absolute favorite way to welcome fall! Picture this: all the cozy spices of pumpkin pie swirled with rich, creamy cheesecake in the most adorable portable package. I first made these for a Halloween party years ago, and now my friends demand them every autumn. The best part? They come together so easily – no fancy piping or decorating skills needed. Just imagine biting through that buttery crumb topping into a moist pumpkin muffin with that surprise pocket of tangy cream cheese filling. Trust me, these disappear FAST whenever I make them!

Table of Contents
Table of Contents
Why You’ll Love These Pumpkin Cheesecake Cupcakes
Listen, these aren’t just any cupcakes – they’re little bites of autumn magic! Here’s why they’ll become your new fall obsession:
- Two desserts in one: All the warmth of pumpkin spice meets the creamy dreaminess of cheesecake – no choosing necessary!
- Perfect for sharing: Portable, mess-free, and guaranteed to wow at bake sales, Thanksgiving dinners, or cozy coffee dates.
- Beginner-friendly: No tricky techniques here – just simple layering that looks way fancier than it actually is.
- That crumb topping: That sweet, cinnamon-kissed crunch takes these from good to “oh-my-gosh-can-I-have-another” status.
Seriously, once you try these, regular pumpkin muffins will just seem… sad.
Ingredients for Pumpkin Cheesecake Cupcakes
Okay, let’s gather our pumpkin-spiced treasures! I’ve broken everything down so you can prep like a pro. Trust me – using exactly what’s listed makes ALL the difference in these cupcakes.
Crumb Topping
- 1/3 cup (67g) packed light or dark brown sugar – packed means really pressed into that measuring cup!
- 1 teaspoon ground cinnamon – the good stuff, none of that dusty old spice jar
- 1/4 cup (4 Tbsp; 56g) unsalted butter, melted – I always use real butter, never margarine
- 2/3 cup (84g) all-purpose flour – spoon it in, then level it off
Pumpkin Muffins
- 1 and 3/4 cups (219g) all-purpose flour – again, spooned & leveled!
- 1 teaspoon baking powder – check that expiration date
- 1 teaspoon baking soda – fresh is best
- 1/2 teaspoon salt – just a pinch to balance the sweetness
- 2 teaspoons ground cinnamon – because pumpkin deserves extra love
- 1 teaspoon pumpkin pie spice – store-bought or homemade (see notes below)
- 1/2 cup (100g) packed brown sugar – dark or light, your choice
- 1/2 cup (100g) granulated sugar – regular white sugar works perfectly
- 2 large eggs, at room temperature – this matters for proper mixing!
- 1 cup (227g) canned pumpkin puree – NOT pumpkin pie filling
- 1/2 cup (120ml) vegetable oil – or melted coconut oil if you prefer
- 1/3 cup (80ml) milk – any percentage works
- 1 teaspoon pure vanilla extract – the real deal, please
Cream Cheese Filling
- 6 ounces (170g) full-fat brick cream cheese – softened to room temp (low-fat won’t give that luscious texture)
- 1 egg yolk, at room temperature – just the yolk for extra richness
- 1/2 teaspoon pure vanilla extract – more vanilla goodness
- 3 Tablespoons (36g) granulated sugar – sweetens the deal
Ingredient Notes & Substitutions
Quick swaps: coconut oil works for vegetable oil, and homemade pumpkin pie spice (mix cinnamon, ginger, nutmeg, allspice) beats store-bought. Must-use: full-fat cream cheese – low-fat versions make the filling weepy. Room temp eggs blend better – just pop cold ones in warm water for 5 minutes!

Equipment You’ll Need
Don’t worry – you probably have everything already! Here’s what you’ll need to make these pumpkin cheesecake cupcakes:
- 12-count muffin pan – standard size, nothing fancy
- Nonstick spray or cupcake liners – I’m team spray for that perfect golden crust
- 2 mixing bowls – one for dry, one for wet ingredients
- Whisk & spatula – my trusty mixing duo
- Measuring cups & spoons – accuracy counts with baking!
- Hand mixer or stand mixer – for that dreamy cream cheese filling
See? Told you it was simple. Now let’s get baking!
How to Make Pumpkin Cheesecake Cupcakes
Alright, let’s dive into the fun part – making these little pockets of pumpkin bliss! Don’t let the layers intimidate you – it’s easier than it looks, and I’ll walk you through every step.
Step-by-Step Instructions
1. Preheat & Prep: Crank that oven to 425°F (218°C) – yes, hotter than usual! This initial blast gives our cupcakes that perfect dome. While it heats, spray your muffin pan or line with cupcake liners. I like using nonstick spray for those crispy edges.
2. Make the Crumb Topping: In a small bowl, mix the brown sugar and cinnamon first. Pour in that melted butter (careful, it’s hot!) and stir until it looks like wet sand. Add flour and mix until crumbly – you want pea-sized pieces. Set this aside – resist nibbling!
3. Whisk Dry Ingredients: In your largest bowl, whisk together flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice. Get out any lumps – nobody wants a mouthful of baking soda!
4. Combine Wet Ingredients: In another bowl, whisk the sugars and eggs until smooth. Add pumpkin puree (make sure it’s not watery!), oil, milk, and vanilla. Whisk until it’s one gorgeous orange batter.
5. Marry Wet & Dry: Pour wet ingredients into dry and gently fold together with a spatula. Stop when just combined – a few flour streaks are okay! Overmixing makes tough cupcakes.
6. Whip Up the Filling: Beat softened cream cheese until smooth (no lumps!). Add egg yolk, vanilla, and sugar, mixing until silky. Taste? Okay, maybe just one tiny taste…

7. Layer Like a Pro: Spoon pumpkin batter into cups until 1/3 full. Add a dollop of cream cheese filling (about 1 Tbsp), then cover with more batter until 3/4 full. Top generously with crumbs and press lightly so they stick.
8. Bake Smart: Bake at 425°F for 5 minutes (this creates that initial rise), then reduce to 350°F without opening the oven! Bake 15-17 more minutes until a toothpick comes out with moist crumbs (not wet batter).
9. Cool Properly: Let cupcakes cool in pan for 10 minutes – this prevents sinking. Then transfer to a rack. Try not to eat them all immediately!
Print
Irresistible Pumpkin Cheesecake Cupcakes in 9 Easy Steps
- Prep Time: 20 minutes
- Cook Time: 22 minutes
- Total Time: 42 minutes
- Yield: 12–14 cupcakes 1x
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Description
Pumpkin cheesecake cupcakes combine the flavors of pumpkin spice and creamy cheesecake in a convenient muffin form. Perfect for fall baking.
Ingredients
- Crumb Topping
- 1/3 cup (67g) packed light or dark brown sugar
- 1 teaspoon ground cinnamon
- 1/4 cup (4 Tbsp; 56g) unsalted butter, melted
- 2/3 cup (84g) all-purpose flour
- Pumpkin Muffins
- 1 and 3/4 cups (219g) all-purpose flour (spooned & leveled)
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 2 teaspoons ground cinnamon
- 1 teaspoon store-bought or homemade pumpkin pie spice
- 1/2 cup (100g) packed light or dark brown sugar
- 1/2 cup (100g) granulated sugar
- 2 large eggs, at room temperature
- 1 cup (227g) canned pumpkin puree
- 1/2 cup (120ml) vegetable oil (or melted coconut oil)
- 1/3 cup (80ml) milk
- 1 teaspoon pure vanilla extract
- Cream Cheese Filling
- 6 ounces (170g) full-fat brick cream cheese, softened to room temperature
- 1 egg yolk, at room temperature
- 1/2 teaspoon pure vanilla extract
- 3 Tablespoons (36g) granulated sugar
Instructions
- Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners.
- Make the crumb topping by mixing brown sugar, cinnamon, melted butter, and flour until crumbly. Set aside.
- Whisk dry ingredients (flour, baking powder, baking soda, salt, cinnamon, pumpkin pie spice) in a large bowl.
- In another bowl, whisk wet ingredients (brown sugar, granulated sugar, eggs, pumpkin, oil, milk, vanilla). Combine wet and dry ingredients without over-mixing.
- Beat cream cheese until smooth, then add egg yolk, vanilla, and sugar to make the filling.
- Layer muffin batter, cheesecake filling, and more batter in muffin cups. Top with crumbs and press lightly.
- Bake at 425°F for 5 minutes, then reduce to 350°F and bake 15-17 minutes. Cool for 10 minutes before serving.
Notes
- Store leftovers tightly covered at room temperature for up to 2 days or refrigerate for up to 1 week.
- Use full-fat cream cheese for best texture.
- Check doneness with a toothpick—crumbs should be moist but not wet.
Nutrition
- Serving Size: 1 cupcake
- Calories: 280
- Sugar: 20g
- Sodium: 180mg
- Fat: 14g
- Saturated Fat: 5g
- Unsaturated Fat: 7g
- Trans Fat: 0g
- Carbohydrates: 35g
- Fiber: 1g
- Protein: 4g
- Cholesterol: 55mg
Tips for Perfect Pumpkin Cheesecake Cupcakes
After making these cupcakes more times than I can count, here are my foolproof tips to guarantee bakery-quality results every time:
- Room temp is key: Cold eggs and cream cheese won’t blend smoothly – take them out at least 30 minutes before baking.
- Don’t overfill: Stick to 3/4 full max – these babies rise! Overflow means messy pans and flat tops.
- The toothpick test: Look for moist crumbs, not wet batter. The filling stays creamy, so check the pumpkin part.
- Storage smarts: Keep airtight at room temp for 2 days, or refrigerate for up to a week. Microwave chilled ones for 10 seconds to revive that fresh-baked magic!
Follow these, and you’ll have coworkers begging for your “secret” recipe!

Serving & Storage
Here’s the best part – these pumpkin cheesecake cupcakes actually get better after cooling! Let them sit for at least 30 minutes so the filling sets, though I won’t judge if you sneak one warm (that melty cheesecake center is *chef’s kiss*). Store leftovers in an airtight container at room temp for 2 days, or pop them in the fridge for up to a week – just microwave chilled ones for 10 seconds to bring back that fresh-baked magic. Pro tip: they’re amazing with a dollop of whipped cream or a drizzle of caramel for extra indulgence!
Nutritional Information
Each pumpkin cheesecake cupcake packs about 280 calories with 20g sugar and 4g protein – not bad for such a decadent treat! Remember, nutrition varies based on exact ingredients used (I’m looking at you, extra crumb topping lovers!). These values are estimates based on standard ingredients.
FAQs About Pumpkin Cheesecake Cupcakes
How long do these cupcakes last in the fridge?
They stay fresh for up to 1 week when stored in an airtight container. Just microwave them for 10 seconds to bring back that just-baked warmth!
How do I know when they’re done baking?
Look for moist crumbs on a toothpick inserted into the pumpkin part – not wet batter. The filling stays creamy, so don’t worry if it looks soft!
Can I use a different pan if I don’t have a muffin tin?
Absolutely! A 9-inch square baking pan works too – just layer batter, filling, and crumbs as usual. Bake at 350°F for 25-30 minutes and cut into squares.
Can I freeze these cupcakes?
Yes! Freeze them (unfrosted) in a single layer, then transfer to a freezer bag. Thaw overnight in the fridge and warm slightly before serving.

Share Your Pumpkin Cheesecake Cupcakes
I’d LOVE to see your creations! Snap a photo of those gorgeous pumpkin cheesecake cupcakes and tag me – nothing makes me happier than seeing you all bake my recipes. Leave a comment below telling me how they turned out (or just to say hi!). Happy baking, friends!
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