The first whiff of autumn brings a cozy nostalgia that can't be ignored, as leaves turn shades of gold and the promise of pumpkin spice fills the air. That's exactly the inspiration behind these delightful Autumn Harvest Cupcakes. Merging the rich flavors of pumpkin with a hidden cheesecake surprise, this recipe is both a crowd-pleaser and a perfect way to embrace the changing seasons. Not only are they easy to whip up in just around 45 minutes, but they also feature a graham cracker crust that adds a delightful crunch to every bite. Whether you're hosting a gathering or simply treating yourself to something special, these cupcakes are sure to impress. Ready to discover the secret to baking joy in every fall-themed bite?
Why are Autumn Harvest Cupcakes a Must-Try?
Seasonal Delight: These cupcakes offer the rich essence of fall with cozy flavors like pumpkin and warm spices, making each bite a celebration of the season.
Surprise Center: Experience a decadent twist with a creamy cheesecake filling that adds a luxurious touch to this easy recipe.
Simple Preparation: With just 45 minutes of prep and bake time, you can enjoy homemade desserts without spending hours in the kitchen.
Perfect for Sharing: Great for gatherings, they’ll easily become the star of your dessert table, appealing to both friends and family alike.
Versatile Pairing: Pair these cupcakes with cider or tea for a perfectly cozy treat any time of day! For more delightful pumpkin recipes, check out our pumpkin spice muffins and pumpkin pie bars for even more fall-inspired comfort.
Autumn Harvest Cupcake Ingredients
For the Crust
- Crushed graham crackers – these lend a delightful crunch and warmth, reminiscent of bonfire nights.
- Dark brown sugar – this enhances the caramel-like depth, making each bite richer.
- Cinnamon – adds that quintessential fall spice aroma we all adore.
- Melted butter – helps to bind the crust and adds a buttery flavor.
For the Cheesecake Filling
- Cream cheese – provides a creamy, luscious texture that perfectly complements the pumpkin.
- Granulated sugar – balances the cream cheese’s tanginess with just the right sweetness.
- Vanilla bean paste – infuses a lovely warmth and flavor that elevates the filling.
For the Pumpkin Batter
- All-purpose flour – the base of your cupcakes, providing structure and stability.
- Baking soda & Baking powder – both are essential to help your cupcakes rise and become fluffy.
- Salt – enhances all the other flavors, making them pop!
- Cinnamon, nutmeg, cloves, ginger – this signature blend of spices creates the warm flavors of fall.
- Large eggs – bind the ingredients together and keep the cupcakes moist.
- Granulated & light brown sugar – a combination adds sweetness and a hint of caramel flavor.
- Canola oil – keeps your cupcakes moist and tender without adding a distinct flavor.
- Pumpkin purée – the star ingredient that gives these Autumn Harvest Cupcakes their delightful taste and vibrant color.
For the Frosting
- Butter – the base for a creamy frosting that spreads beautifully.
- Sour cream – adds a tangy flavor and helps create a fluffy texture.
- Vanilla – a simple addition that elevates the flavor profile of your frosting.
- Powdered sugar – sweetens your frosting and gives it the perfect consistency for piping.
For the Topping
- Crushed graham cracker crumbs – sprinkle these on top for an extra bit of crunch and a charming finishing touch!
These Autumn Harvest Cupcake ingredients come together to create an unforgettable treat that celebrates the flavors of the season. Enjoy the process, and let the warmth of your kitchen fill the air!
Step‑by‑Step Instructions for Autumn Harvest Cupcakes
Step 1: Prepare the Graham Cracker Crust
In a mixing bowl, combine 1 ½ cups of crushed graham crackers, ½ cup dark brown sugar, 1 teaspoon of cinnamon, and ½ cup melted butter until you achieve a sandy and moist texture. Use about 1 tablespoon of this mixture to press into the bottom of each cupcake liner, forming the base for your delicious Autumn Harvest Cupcakes.
Step 2: Make the Cheesecake Filling
In a separate bowl, beat 8 oz of softened cream cheese with ½ cup granulated sugar and 1 teaspoon of vanilla bean paste until smooth and creamy. Once well combined, transfer this delightful mixture into a piping bag, preparing it to add a luscious surprise to each cupcake.
Step 3: Mix the Dry Ingredients
In a clean bowl, whisk together 1 ½ cups all-purpose flour, 1 teaspoon baking soda, 1 teaspoon baking powder, ½ teaspoon salt, 1 teaspoon of cinnamon, ½ teaspoon of nutmeg, ½ teaspoon of cloves, and ½ teaspoon of ginger. This aromatic blend will bring the essence of fall to your Autumn Harvest Cupcakes.
Step 4: Combine Wet Ingredients
In a large mixing bowl, whisk together 4 large eggs, ¾ cup granulated sugar, ½ cup light brown sugar, ½ cup canola oil, and 15 oz of pumpkin purée until the mixture is smooth and homogenous. This will be the moist base for your cupcakes, perfectly complementing the spices.
Step 5: Fold Dry Ingredients into Wet Mixture
Carefully fold the dry ingredients from Step 3 into the wet mixture from Step 4 just until combined; avoid overmixing to ensure your cupcakes remain light and fluffy. The batter should be thick but smooth, ready to be poured into your prepared cupcake liners.
Step 6: Fill the Cupcake Liners
Fill each cupcake liner halfway with the pumpkin batter and then pipe approximately 1-2 teaspoons of the cheesecake filling into the center of each. Top off each liner with more pumpkin batter until they’re about ¾ full, creating a layered effect in your Autumn Harvest Cupcakes.
Step 7: Bake the Cupcakes
Preheat your oven to 350 °F (175 °C). Bake the cupcakes for 18–22 minutes or until they are set and a toothpick inserted into the center comes out mostly clean. Once baked, allow the cupcakes to cool completely on a wire rack before frosting.
Step 8: Make the Frosting
In a mixing bowl, beat 1 cup of softened butter until creamy. Add ½ cup sour cream and 2 teaspoons of vanilla, mixing well to combine. Gradually incorporate 4 ½ cups of powdered sugar while beating until the frosting is smooth and fluffy, ready for decorating your Autumn Harvest Cupcakes.
Step 9: Decorate the Cupcakes
Transfer the frosting to a piping bag and pipe it onto the cooled cupcakes, creating beautiful swirls of sweet goodness. Finish by sprinkling crushed graham cracker crumbs on top for added texture, perfectly enhancing the flavor and theme of your festive Autumn Harvest Cupcakes.
Autumn Harvest Cupcakes Variations & Substitutions
Feel free to let your creativity shine by customizing these delightful cupcakes to suit your tastes!
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Gluten-Free: Substitute all-purpose flour with a gluten-free baking mix for deliciously autumnal cupcakes without the gluten.
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Dairy-Free: Use vegan cream cheese and coconut oil instead of butter in the frosting. You'll enjoy the same creamy richness without dairy.
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Spiced Twist: Add a pinch of cayenne pepper to the pumpkin batter for a sweet-and-spicy surprise that warms you from within. This unexpected kick will have everyone asking for the secret ingredient!
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Nutty Addition: Fold in ½ cup of chopped nuts like walnuts or pecans for added crunch and flavor, bringing a lovely texture and warmth to every bite.
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Frosting Flavor: Experiment with different flavors in your frosting by adding a tablespoon of maple syrup or orange zest for a refreshing twist. It’s a simple way to elevate the overall cupcake experience.
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Pumpkin Swap: For a twist on flavors, replace pumpkin purée with mashed bananas for a unique banana-pumpkin fusion that’s equally moist and delicious.
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Lower Sugar: Reduce the granulated sugar by ¼ cup in the cupcake batter for a slightly less sweet treat, while still enjoying a satisfying dessert experience.
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Coconut Topping: Sprinkle shredded coconut on top instead of graham cracker crumbs for a tropical flair that complements the warm spices beautifully.
These variations not only personalize your cupcakes but can also cater to various dietary preferences, making them perfect for any celebration. For more delightful pumpkin recipes, check out our pumpkin spice muffins and pumpkin pie bars that will surely warm your home this season!
How to Store and Freeze Autumn Harvest Cupcakes
Room Temperature: Keep freshly baked cupcakes at room temperature for up to 2 days in an airtight container to maintain softness and flavor.
Fridge: If you want to extend their freshness, store the Autumn Harvest Cupcakes in the fridge for up to 5 days, ensuring they are covered to prevent drying out.
Freezer: For longer storage, freeze unfrosted cupcakes for up to 3 months. Wrap individually in plastic wrap and place in a sealed freezer bag to prevent freezer burn.
Reheating: To enjoy leftovers, warm the cupcakes in the microwave for about 10-15 seconds, then frost if desired, for a delightful treat anytime!
What to Serve with Autumn Harvest Cupcakes?
Imagine delighting your family and friends with a spread that perfectly complements your seasonal treats, embracing the cozy embrace of fall.
- Warm Apple Cider: This comforting drink enhances the spiced pumpkin flavors, evoking a cozy autumn atmosphere with each sip.
- Spiced Tea: A fragrant brew with hints of cinnamon and clove perfectly echoes the spices in your cupcakes, adding warmth and depth.
- Cranberry Sauce: The tartness of cranberry counterbalances the sweetness of the cupcakes, providing a refreshing contrast in flavor.
- Caramel Sauce: Drizzling warm caramel adds a luxurious touch that beautifully complements the graham cracker crust and creamy filling.
- Roasted Butternut Squash Salad: A vibrant salad with roasted squash and almonds brings a fresh, crunchy element to your dessert table.
- Chocolate Chip Cookies: For an added sweet treat, classic cookies serve as a nostalgic comfort alongside the cupcakes.
- Vanilla Bean Ice Cream: The creaminess of the ice cream pairs wonderfully with the warm cupcakes, creating a delightful dessert duo.
- Pumpkin Spice Latte: Embrace the fall vibes with this iconic drink, as its flavors blend perfectly with the rich pumpkin notes in the cupcakes.
- Hibiscus Iced Tea: A refreshing drink option that adds a colorful touch while balancing the richness of your festive dessert.
Make Ahead Options
These Autumn Harvest Cupcakes are perfect for meal prep, allowing you to enjoy the cozy flavors of fall without the last-minute rush! You can prepare the graham cracker crust and cheesecake filling up to 24 hours in advance; simply store each component separately in airtight containers in the refrigerator to maintain their quality. On the day of serving, just mix the cupcake batter and fill the liners, then bake as directed. To ensure your cupcakes stay fresh, frost them shortly before serving to keep the frosting fluffy and delicious. With these make-ahead options, you’ll have delightful treats ready to impress your family and friends with minimal effort!
Expert Tips for Autumn Harvest Cupcakes
Perfect Crust: Ensure your graham cracker crust is firmly pressed into the liners; this will provide a stable base and prevent the crust from crumbling.
Cheesecake Filling: Pipe the cheesecake filling gently to avoid excess pressure that could cause it to overflow during baking; a small amount goes a long way!
Batter Folding: When combining dry and wet ingredients, fold gently and stop as soon as combined to maintain a light and airy texture in your cupcakes.
Baking Check: Use a toothpick to check if your cupcakes are done; they should come out mostly clean, indicating they're baked perfectly without being dry.
Cooling Time: Allow your cupcakes to cool completely before frosting to prevent the frosting from melting; patience here will lead to beautifully decorated treats.
Flavor Pairings: Serve your Autumn Harvest Cupcakes with warm cider or a spiced latte to enhance the cozy festive experience!
Autumn Harvest Cupcakes Recipe FAQs
How do I choose the right pumpkin puree?
When selecting pumpkin puree, look for 100% pure pumpkin in a can without any added sugars or spices. If using fresh pumpkin, choose a sugar pumpkin for its sweetness and creamy texture. It should feel firm with no soft spots, and when you cut it open, the flesh should be bright orange and flavorful.
What’s the best way to store leftover cupcakes?
To keep your Autumn Harvest Cupcakes fresh, store them in an airtight container at room temperature for up to 2 days. If you’d like to keep them longer, place them in the fridge, ensuring they're covered to avoid drying out. They can last up to 5 days this way.
Can I freeze the cupcakes?
Absolutely! For freezing, it’s best to freeze the unfrosted cupcakes. Wrap each cupcake tightly in plastic wrap and place them in a sealed freezer bag. This method will keep them fresh for up to 3 months. To enjoy them, simply thaw them at room temperature and frost them once they are soft.
What should I do if my cupcakes sink in the middle?
If your cupcakes sink, it may be due to undermixing or overmixing the batter. Ensure you fold the dry ingredients into the wet ingredients gently until just combined. Also, check that your baking soda and baking powder are fresh, as expired leavening agents can prevent proper rising.
Can I make these cupcakes gluten-free?
Yes! To make gluten-free Autumn Harvest Cupcakes, substitute the all-purpose flour with a gluten-free flour blend. Make sure it contains a binding agent like xanthan gum for best results. Additionally, double-check that your other ingredients are gluten-free, particularly any processed items.
Are these cupcakes safe for pets?
While the ingredients in Autumn Harvest Cupcakes are safe for most humans, they are not suitable for pets. The sugar and butter content can be harmful to dogs and other pets. If you're enjoying these treats, be sure to keep them out of reach from your furry friends!

Autumn Harvest Cupcakes: Cozy Flavors for Fall Celebrations
Equipment
- mixing bowl
- Piping bag
- whisk
- Oven
- wire rack
Ingredients
For the Crust
- 1.5 cups crushed graham crackers these lend a delightful crunch and warmth
- 0.5 cups dark brown sugar enhances the caramel-like depth
- 1 teaspoon cinnamon adds the quintessential fall spice aroma
- 0.5 cups melted butter helps to bind the crust
For the Cheesecake Filling
- 8 oz cream cheese provides a creamy texture
- 0.5 cups granulated sugar balances the cream cheese's tanginess
- 1 teaspoon vanilla bean paste infuses a lovely warmth and flavor
For the Pumpkin Batter
- 1.5 cups all-purpose flour provides structure and stability
- 1 teaspoon baking soda helps your cupcakes rise
- 1 teaspoon baking powder essential for fluffiness
- 0.5 teaspoon salt enhances the other flavors
- 1 teaspoon cinnamon part of the signature spice blend
- 0.5 teaspoon nutmeg adds fall flavor
- 0.5 teaspoon cloves enhances the warm flavors
- 0.5 teaspoon ginger another element of warm spices
- 4 large eggs bind the ingredients
- 0.75 cups granulated sugar adds sweetness
- 0.5 cups light brown sugar adds a hint of caramel flavor
- 0.5 cups canola oil keeps the cupcakes moist
- 15 oz pumpkin purée the star ingredient
For the Frosting
- 1 cup butter base for creamy frosting
- 0.5 cups sour cream adds tangy flavor
- 2 teaspoons vanilla elevates the flavor profile
- 4.5 cups powdered sugar sweetens and thickens the frosting
For the Topping
- 0.5 cups crushed graham cracker crumbs for an extra bit of crunch
Instructions
Step‑by‑Step Instructions
- Prepare the Graham Cracker Crust: Combine crushed graham crackers, dark brown sugar, cinnamon, and melted butter until sandy and moist. Press about 1 tablespoon into each cupcake liner.
- Make the Cheesecake Filling: Beat cream cheese, granulated sugar, and vanilla bean paste until smooth. Transfer to piping bag.
- Mix the Dry Ingredients: Whisk together all-purpose flour, baking soda, baking powder, salt, cinnamon, nutmeg, cloves, and ginger.
- Combine Wet Ingredients: Whisk eggs, granulated sugar, light brown sugar, canola oil, and pumpkin purée until smooth.
- Fold Dry Ingredients: Carefully fold dry ingredients into the wet mixture until combined, ensuring the batter is thick but smooth.
- Fill the Cupcake Liners: Fill liners halfway with pumpkin batter, pipe cheesecake filling into the center, then top with more batter until ¾ full.
- Bake the Cupcakes: Preheat oven to 350°F (175°C). Bake for 18–22 minutes until set. Cool on a wire rack.
- Make the Frosting: Beat softened butter until creamy, add sour cream and vanilla, then gradually mix in powdered sugar until smooth.
- Decorate the Cupcakes: Pipe frosting onto cooled cupcakes and sprinkle with crushed graham cracker crumbs.
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