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Delectable Autumn Harvest Cupcakes to Cozy Up Your Fall

Published: Sep 16, 2025 by Emma Saviani ·

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There’s something so magical about autumn that calls for cozy sweets, and these Autumn Harvest Cupcakes are my heartfelt response to that seasonal spirit. Imagine walking through crisp leaves, with the scent of pumpkin and warm spices in the air—this recipe brings that comforting feeling right into your kitchen. With just 45 minutes of your time, you can whip up these delightful treats that showcase the rich flavor of pumpkin mixed with a dreamy cream cheese center. They’re not only a crowd-pleaser but also perfect for batch-making to share with friends or enjoy over a breezy weekend. So, are you ready to embrace the season and create something unforgettable? Let's dive into this delicious journey together!

Autumn Harvest Cupcakes

Why Are Autumn Harvest Cupcakes Irresistible?

Comforting Flavors: The harmonious blend of pumpkin puree, spices, and a creamy cheesecake center wraps each bite in warmth and nostalgia, perfect for cozy autumn days.

Easy to Make: With just 45 minutes total time, these cupcakes are simple enough for any home cook—great for those new to baking!

Batch-Friendly: Whether for a fall gathering or just to enjoy with family, this recipe is easily doubled or tripled to satisfy a crowd.

Visual Appeal: Topped with fluffy frosting and garnished with crushed graham crackers, they look as delightful as they taste, making them perfect for any occasion.

Get ready to impress your loved ones with these delightful treats that capture the essence of the season. Be sure to check out our tips for successful baking to enhance your cupcake-making experience!

Autumn Harvest Cupcake Ingredients

For the Crust

• Crushed graham crackers – Provide a delightful crunch that complements the creamy filling.
• Dark brown sugar – Enhances the crust with a rich, caramel-like flavor.
• Cinnamon – Adds a warm and aromatic spice that hints at the flavors of the season.
• Melted butter – Binds the crust ingredients together for a perfect, buttery blend.

For the Cheesecake Filling

• Cream cheese – Creates a luscious, creamy center that's the star of these Autumn Harvest Cupcakes.
• Granulated sugar – Balances the tanginess of the cream cheese for a sweet delight.
• Vanilla bean paste – Infuses the filling with aromatic vanilla, enhancing the flavor profile.

For the Cupcake Batter

• All-purpose flour – Forms the base of the cupcakes, providing structure.
• Baking soda – Helps the cupcakes rise to the perfect fluffy texture.
• Baking powder – Works alongside baking soda for further leavening.
• Salt – Enhances the sweetness and overall flavor of the cupcakes.
• Cinnamon – Reinforces the warm spice theme throughout the batter.
• Nutmeg – Adds an additional layer of warmth, reminiscent of cozy autumn vibes.
• Cloves – Imparts a hint of earthiness that pairs beautifully with pumpkin.
• Ginger – Infuses a gentle spiciness, making each bite a flavor adventure.
• Large eggs – Provide moisture and richness, ensuring a tender crumb.
• Granulated sugar – Sweetens the batter for a delectable treat.
• Light brown sugar – Adds depth of flavor with its molasses undertones.
• Canola oil – Keeps the cupcakes moist and light.
• Pumpkin purée – The star ingredient that gives these cupcakes their seasonal charm.
• Sour cream – Adds moisture and a subtle tang, keeping cupcakes tender.

For the Frosting

• Butter – Provides a creamy base for rich frosting.
• Sour cream – Enhances the flavor and lightness of the frosting.
• Powdered sugar – Sweetens and thickens the frosting to the perfect spreadable consistency.

Step‑by‑Step Instructions for Autumn Harvest Cupcakes

Step 1: Prepare the Crust
In a mixing bowl, combine 1 ½ cups of crushed graham crackers, ⅓ cup of dark brown sugar, ½ teaspoon of cinnamon, and ½ cup of melted butter until the mixture resembles sandy crumbs. Use about 1 tablespoon of this crust mixture to press firmly into the bottom of each cupcake liner—this forms a delightful base for your Autumn Harvest Cupcakes.

Step 2: Make the Cheesecake Filling
In a clean bowl, beat 8 oz of softened cream cheese, ½ cup of granulated sugar, and 1 teaspoon of vanilla bean paste until smooth and creamy. Once combined, transfer this luscious mixture into a piping bag for easy filling later. Set the piping bag aside while you prepare the cupcake batter, keeping the filling rich and delectable.

Step 3: Prepare the Pumpkin Batter
In one bowl, whisk together 2 cups of all-purpose flour, 1 teaspoon of baking soda, 1 teaspoon of baking powder, ½ teaspoon of salt, 1 teaspoon of cinnamon, ½ teaspoon of nutmeg, ½ teaspoon of cloves, and ½ teaspoon of ginger. In a large mixing bowl, whisk together 3 large eggs, 1 cup of granulated sugar, ¾ cup of light brown sugar, ½ cup of canola oil, and 15 oz of pumpkin purée until the mixture is smooth. Carefully fold in the dry ingredients just until combined—this will keep your Autumn Harvest Cupcakes light and fluffy.

Step 4: Assemble the Cupcakes
Fill each cupcake liner halfway with the pumpkin batter, ensuring a nice even layer. Then, carefully pipe about 1–2 teaspoons of the cheesecake filling into the center of each filled liner. Top with more pumpkin batter until the liners are filled to about ¾ full, giving your Autumn Harvest Cupcakes that perfect layered look.

Step 5: Bake the Cupcakes
Preheat your oven to 350°F (175°C). Once preheated, place your filled cupcake liners in the oven and bake for 18–22 minutes. The cupcakes are done when they are set and a toothpick inserted comes out mostly clean. Allow them to cool completely on a wire rack, letting the delicious aromas fill your kitchen.

Step 6: Make the Frosting
In a mixing bowl, beat ½ cup of softened butter until creamy and smooth. Gradually mix in ½ cup of sour cream and 1 teaspoon of vanilla until well combined. Slowly add 3 cups of powdered sugar while beating until the frosting is fluffy and smooth, perfect for decorating your cooled Autumn Harvest Cupcakes.

Step 7: Decorate the Cupcakes
Transfer your fluffy frosting into a piping bag and pipe it generously onto each cupcake. For an extra touch, sprinkle the tops with crushed graham cracker crumbs, adding texture and a seasonal flair. Serve these delightful Autumn Harvest Cupcakes alongside cider, tea, or coffee for a warming fall treat that’s sure to impress!

Autumn Harvest Cupcakes

How to Store and Freeze Autumn Harvest Cupcakes

Room Temperature: Store unfrosted Autumn Harvest Cupcakes in an airtight container for up to 2 days to keep them fresh and moist.

Fridge: If you have leftover frosted cupcakes, keep them in the refrigerator for up to 5 days. Make sure they’re covered to prevent them from drying out.

Freezer: For longer storage, freeze unfrosted cupcakes in an airtight container for up to 3 months. Thaw in the fridge overnight before frosting and serving.

Reheating: If you'd like to enjoy them warm, pop your cupcake in the microwave for about 10-15 seconds—just until warm and inviting!

Make Ahead Options

These Autumn Harvest Cupcakes are fantastic for meal prep, allowing busy home cooks to get a head start on their baking! You can prepare the crust and cheesecake filling up to 24 hours in advance. Simply store the crust mixture tightly wrapped in the refrigerator, and keep the cheesecake filling in a piping bag, refrigerated until needed. You can also make the cupcake batter and fill the liners up to 3 days ahead; just cover with plastic wrap to ensure they stay fresh. When ready to bake, simply preheat the oven and pop them in, and you’ll have warm, delicious cupcakes that taste just as delightful as if you made them on the spot!

What to Serve with Autumn Harvest Cupcakes

Imagine the comforting scent of spices filling the air as you prepare to indulge in these delicious autumn-inspired treats.

  • Warm Apple Cider: The sweet and spiced notes of apple cider create a cozy pairing with the pumpkin and cream cheese flavors.
  • Vanilla Ice Cream: A scoop of creamy vanilla ice cream melts into the warm cupcake, making each bite decadently delightful.
  • Maple Pecan Tart: This dessert's crunchy pecans and sweet maple syrup beautifully complement the rich flavors of the cupcakes.
  • Roasted Butternut Squash Soup: The creamy and earthy soup provides a savory contrast that balances the sweetness of the cupcakes, perfect for fall gatherings.
  • Chai Tea: The warming spices of chai tea enhance the flavors in the cupcakes while offering a soothing beverage to sip alongside.
  • Dark Chocolate Coffee: The rich, bold flavors of dark chocolate coffee provide an indulgent backdrop, elevating your cupcake experience.
  • Candied Nuts: A side of sweet, crunchy nuts adds satisfying texture and a lovely contrast to the soft, moist cupcakes.
  • Spiced Pear Salad: A fresh salad with spiced pears offers a refreshing and fruity element that balances the sweetness of the Autumn Harvest Cupcakes.
  • Caramel Sauce: Drizzle some warm caramel over each cupcake for an extra touch of decadence that will leave your guests wanting more.

Autumn Harvest Cupcakes Variations

Feel free to unleash your creativity and customize these cupcakes to match your taste buds!

  • Gluten-Free: Swap all-purpose flour for a gluten-free blend to make these cupcakes suitable for gluten-sensitive friends.
    Experience the same warm flavors without worry, as many gluten-free mixes work beautifully in baked goods!

  • Nut-Free: Replace the ground spices with a sprinkle of nutmeg or extra cinnamon if you're avoiding nuts altogether.
    This ensures nobody misses out on flavor while keeping it safe for those with allergies.

  • Dairy-Free: Use vegan cream cheese and plant-based butter to create a dairy-free version that’s still creamy and rich.
    Your loved ones won’t even know they’re enjoying a dairy-free treat!

  • Spiced Up: Add a pinch of cayenne pepper or a bit of chili powder to the batter for a surprising kick of flavor.
    That little hint of heat will dance on your palate and add an exciting twist!

  • Pumpkin Spice Latte Twist: Incorporate a tablespoon of instant coffee granules into the batter for a caffeinated boost.
    Pair these cupcakes with your favorite fall drink for the ultimate cozy treat!

  • Frosting Flavor Boost: Infuse the frosting with maple extract or a splash of bourbon for a deeper, richer flavor.
    This buttery frosting won’t just be sweet; it'll have a delightful twist that your guests will love!

  • Add-ins: Fold in chocolate chips or toasted pecans into the batter for additional texture and flavor fun.
    Each bite will be filled with surprises, leading to a delightful crunch amidst the moist cake.

  • Mini Cupcake Variation: Bake these as mini cupcakes to create bite-sized treats perfect for parties or snacking.
    Everyone will enjoy indulging in two or three of these small, sweet goodies!

Feel free to explore these variations, and check out our tips on how to perfect your frosting and make the most of seasonal flavors for a memorable baking experience!

Helpful Tricks for Autumn Harvest Cupcakes

  • Crust Consistency: Ensure your graham cracker mixture is sand-like and moist before pressing it into the liners. A too-dry crust might crumble.

  • Cheesecake Filling: Don’t skip the piping bag! It makes adding the cream cheese filling effortless, ensuring each cupcake gets a delightful center.

  • Fold Gently: When combining wet and dry ingredients, be gentle! Overmixing can lead to tough cupcakes rather than the fluffy texture you're aiming for.

  • Oven Thermometer: Check your oven's temperature with a thermometer. An incorrect temperature may lead to unevenly baked Autumn Harvest Cupcakes.

  • Cooling Time: Allow cupcakes to cool completely before frosting. This prevents the frosting from melting and helps maintain that beautiful shape!

  • Storage Tips: If making ahead, store unfrosted cupcakes in an airtight container at room temperature for up to 2 days. Frost when ready to serve for the best freshness.

Autumn Harvest Cupcakes

Autumn Harvest Cupcakes Recipe FAQs

What type of pumpkin puree should I use?
Absolutely! I recommend using canned pumpkin puree because it offers a consistent texture and flavor. Look for 100% pure pumpkin, not pumpkin pie filling, which contains added sugars and spices. If you're feeling adventurous, you can also roast and puree fresh pumpkin for a homemade touch—just ensure it's very smooth!

How should I store leftover cupcakes?
Very good question! Store any leftover frosted Autumn Harvest Cupcakes in an airtight container in the refrigerator for up to 5 days. This will keep them fresh and prevent the frosting from drying out. If you're keeping them unfrosted, you can store them on the kitchen counter in a sealed container for up to 2 days before frosting.

Can I freeze these cupcakes?
Certainly! To freeze your cupcakes, first ensure they are completely cool. Then, place them in an airtight container or wrap them individually in plastic wrap, followed by aluminum foil for extra protection. They can be frozen for up to 3 months. When you're ready to enjoy, simply thaw them in the refrigerator overnight before adding frosting.

What should I do if my cupcake batter is too thick?
If you find that your cupcake batter is too thick, don't worry! Just add a tablespoon or two of milk to loosen it up. This will help maintain that delightful light texture we aim for in these Autumn Harvest Cupcakes. Remember to fold gently when mixing; overmixing can lead to a denser cupcake.

Are these cupcakes suitable for people with allergies?
Good question! These delightful cupcakes contain common allergens like eggs, dairy (in the cream cheese and butter), and gluten (in the all-purpose flour). For a substitute, you could try using egg replacer and dairy-free cream cheese for an allergy-friendly version. Always check labels for hidden allergens!

How can I avoid overbaking my cupcakes?
To prevent overbaking, start checking your cupcakes at the 18-minute mark. Insert a toothpick into the center; if it comes out with a few moist crumbs but no wet batter, they’re done! Remember, they continue to cook slightly after being removed from the oven, so it’s better to err on the side of caution!

Autumn Harvest Cupcakes

Delectable Autumn Harvest Cupcakes to Cozy Up Your Fall

Delicious Autumn Harvest Cupcakes featuring pumpkin and warm spices, perfect for the fall season.
Print Pin Rate
Course: Dessert
Cuisine: American
Keyword: Autumn Harvest Cupcakes, Baking, cozy treats, Cupcakes, fall desserts, pumpkin
Prep Time: 15 minutes minutes
Cook Time: 25 minutes minutes
Cooling Time: 10 minutes minutes
Total Time: 45 minutes minutes
Servings: 12 cupcakes
Calories: 290kcal

Equipment

  • Mixing bowl
  • Piping bag
  • Whisk
  • Oven
  • Cupcake liners

Ingredients

For the Crust

  • 1.5 cups crushed graham crackers Provide a delightful crunch that complements the creamy filling.
  • 0.33 cups dark brown sugar Enhances the crust with a rich, caramel-like flavor.
  • 0.5 teaspoon cinnamon Adds a warm and aromatic spice.
  • 0.5 cups melted butter Binds the crust ingredients together.

For the Cheesecake Filling

  • 8 oz cream cheese Creates a luscious, creamy center.
  • 0.5 cups granulated sugar Balances the tanginess of the cream cheese.
  • 1 teaspoon vanilla bean paste Infuses the filling with aromatic vanilla.

For the Cupcake Batter

  • 2 cups all-purpose flour Forms the base of the cupcakes.
  • 1 teaspoon baking soda Helps the cupcakes rise.
  • 1 teaspoon baking powder Works alongside baking soda for further leavening.
  • 0.5 teaspoon salt Enhances overall flavor.
  • 1 teaspoon cinnamon Reinforces the warm spice theme.
  • 0.5 teaspoon nutmeg Adds an additional layer of warmth.
  • 0.5 teaspoon cloves Imparts a hint of earthiness.
  • 0.5 teaspoon ginger Infuses a gentle spiciness.
  • 3 large eggs Provide moisture and richness.
  • 1 cups granulated sugar Sweetens the batter.
  • 0.75 cups light brown sugar Adds depth of flavor.
  • 0.5 cups canola oil Keeps the cupcakes moist.
  • 15 oz pumpkin purée The star ingredient.
  • 0.5 cups sour cream Adds moisture and a subtle tang.

For the Frosting

  • 0.5 cups butter Provides a creamy base.
  • 0.5 cups sour cream Enhances the flavor of the frosting.
  • 3 cups powdered sugar Sweetens and thickens the frosting.

Instructions

Step-by-Step Instructions

  • In a mixing bowl, combine 1 ½ cups of crushed graham crackers, ⅓ cup of dark brown sugar, ½ teaspoon of cinnamon, and ½ cup of melted butter until the mixture resembles sandy crumbs. Use about 1 tablespoon of this crust mixture to press firmly into the bottom of each cupcake liner.
  • In a clean bowl, beat 8 oz of softened cream cheese, ½ cup of granulated sugar, and 1 teaspoon of vanilla bean paste until smooth and creamy. Transfer this mixture into a piping bag for filling later.
  • In one bowl, whisk together 2 cups of all-purpose flour, 1 teaspoon of baking soda, 1 teaspoon of baking powder, ½ teaspoon of salt, 1 teaspoon of cinnamon, ½ teaspoon of nutmeg, ½ teaspoon of cloves, and ½ teaspoon of ginger. In a large mixing bowl, whisk together 3 large eggs, 1 cup of granulated sugar, ¾ cup of light brown sugar, ½ cup of canola oil, and 15 oz of pumpkin purée until smooth. Fold in the dry ingredients just until combined.
  • Fill each cupcake liner halfway with pumpkin batter, then pipe about 1–2 teaspoons of cheesecake filling into the center. Top with more pumpkin batter until the liners are ¾ full.
  • Preheat your oven to 350°F. Place your filled cupcake liners in the oven and bake for 18–22 minutes, until set and a toothpick comes out mostly clean. Allow them to cool completely on a wire rack.
  • In a mixing bowl, beat ½ cup of softened butter until creamy. Gradually mix in ½ cup of sour cream and 1 teaspoon of vanilla until well combined. Slowly add 3 cups of powdered sugar until fluffy and smooth.
  • Transfer your fluffy frosting into a piping bag and pipe it generously onto each cupcake. Sprinkle with crushed graham cracker crumbs for an extra touch.

Notes

Store unfrosted cupcakes in an airtight container for up to 2 days. Frost when ready to serve for freshness.

Nutrition

Serving: 1cupcake | Calories: 290kcal | Carbohydrates: 40g | Protein: 3g | Fat: 14g | Saturated Fat: 8g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 4g | Cholesterol: 40mg | Sodium: 200mg | Potassium: 180mg | Fiber: 1g | Sugar: 20g | Vitamin A: 400IU | Calcium: 30mg | Iron: 1mg

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Ellie Monroe

I’m Ellie, a 54-year-old home cook who believes the best recipes come from the heart. At Heavenly Recipe, I share comforting classics, sweet treats, and simple meals that anyone can make, just like the ones passed down through my family.

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