Name: Gingerbread Whoopie Pies with Cream Cheese Filling Recipe
Prep time: 2 h 45 min
Cook time: 14 min
Total time: 3 h 30 min
Cuisine: American
Ingredients: 2 and 1/4 cups all-purpose flour (281g, spooned & leveled); 2 teaspoons ground ginger; 2 teaspoons ground cinnamon; 1/2 teaspoon ground nutmeg; 1/2 teaspoon ground cloves; 1 teaspoon baking soda; 1/2 teaspoon baking powder; 1/2 teaspoon salt; 6 Tablespoons unsulphured or dark molasses (90ml); 1/4 cup hot water (60ml); 2/3 cup granulated sugar (130g); 1/2 cup vegetable oil (120ml); 1 large egg, at room temperature; 6 ounces full-fat brick cream cheese, softened (170g); 1/4 cup unsalted butter, softened (4 Tbsp; 56g); 1 and 1/2 cups confectioners’ sugar, sifted (180g); 1/2 teaspoon pure vanilla extract; Small pinch of ground ginger; Small pinch of ground cinnamon; Small pinch of ground nutmeg; Small pinch of ground cloves

There’s something instantly cozy and nostalgic about Gingerbread Whoopie Pies, and when you add that luscious cream cheese filling, it’s basically a hug you can eat. This Gingerbread Whoopie Pies with Cream Cheese Filling Recipe is a fantastic blend of warm spices and tangy sweetness that makes any day feel like a holiday.

The image shows a close-up view of nine sandwich cookies stacked closely together in three rows and three columns. Each cookie has two soft, round layers with a rough texture and warm brown color, like gingerbread or molasses. Between each pair of cookie layers, there is a thick middle layer of creamy white filling that is smooth and slightly shiny. The white cream is evenly spread and slightly visible from the sides, making a clear contrast with the dark cookies. The background is a white marbled texture, emphasizing the warm colors of the cookies. photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Gingerbread Whoopie Pies with Cream Cheese Filling Recipe
Top Tip
How to Serve Gingerbread Whoopie Pies with Cream Cheese Filling Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Gingerbread Whoopie Pies with Cream Cheese Filling Recipe

Why You'll Love This Recipe

I remember the first time I baked these whoopie pies; the kitchen smelled like Thanksgiving, and the soft, cakey cookies sandwiching that creamy filling were an instant hit. This recipe brings together the best of gingerbread’s spicy warmth and cream cheese’s richness in a way that's just perfect for sharing.

Perfect Texture: The cookies are soft, cakey, and slightly chewy — not cake, not cookie, but the best of both worlds.
Balanced Spice: The combination of ginger, cinnamon, nutmeg, and cloves gives a cozy, aromatic flavor without overwhelming your palate.
Rich Filling: Cream cheese filling with a subtle hint of the same spices ties the whole pie together in a beautifully balanced way.
Make-Ahead Friendly: You can prep parts ahead of time and even freeze these pies, perfect for easy holiday hosting or last-minute treats.

Ingredients & Why They Work

Every ingredient in this Gingerbread Whoopie Pies with Cream Cheese Filling Recipe plays its part, from the warm spices that evoke holiday memories to the molasses that provides deep flavor and moisture. Here’s a quick rundown of what’s going in and why it matters:

Flat lay of a small pile of all-purpose flour spooned neatly on a white ceramic plate, a small white bowl filled with dark molasses, a small white bowl of hot water, a small white bowl of granulated sugar, a small white bowl of vegetable oil, one large whole uncracked brown egg, a whole block of cream cheese with a smooth surface, a small white bowl of unsalted butter cubes, a small white bowl of sifted confectioners’ sugar, fresh whole sticks of cinnamon, a fresh piece of ginger root, whole nutmeg and whole cloves arranged symmetrically on a simple white ceramic plate, all ingredients fresh and natural, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

All-purpose flour: The base that gives structure but keeps the cookies light and tender.
Ground ginger, cinnamon, nutmeg, cloves: Classic warm spices that create that signature gingerbread flavor in both cookie and filling.
Baking soda and baking powder: Together, they ensure the cookies rise just right and stay soft.
Molasses: Adds moisture, richness, and that distinct, slightly smoky sweetness — I recommend unsulphured or dark molasses like Grandma's brand.
Vegetable oil: Keeps the cookies tender and moist without heaviness.
Granulated sugar: Balances the robust flavor of molasses with a touch of sweetness.
Hot water: Helps dissolve the molasses and brings the dough together.
Egg: Adds binding and richness for a chewy, cakey texture.
Cream cheese (full-fat): The star of the filling — tangy and smooth, it contrasts the spice perfectly.
Unsalted butter: Adds creaminess and helps firm up the filling.
Confectioners’ sugar: Gives the filling the right sweetness and delicate texture without grit.
Vanilla extract: Adds depth and rounds out the filling flavor.

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Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

While I adore the classic spice combo, I always encourage you to tweak this Gingerbread Whoopie Pies with Cream Cheese Filling Recipe based on your tastes or what you have on hand. It’s all about making it feel like home for you.

Spice it up or down: If you like things a bit bolder, add a touch more ginger or cinnamon. Or dial back if you prefer a subtler hint.
Vegan version: You can swap cream cheese with vegan cream cheese and use a flax egg or commercial egg replacer for the cookie batter.
Molasses substitute: If you don’t have molasses, a mix of dark brown sugar with a little honey can mimic the depth, though it won’t be the same.
Smaller portions: Try making mini whoopie pies — they’re fun for parties and always disappear fast!

Step-by-Step: How I Make Gingerbread Whoopie Pies with Cream Cheese Filling Recipe

The image shows several soft, round brown sandwich cookies with a rough, slightly cracked texture on top. Each sandwich cookie is made of two cookie layers with a thick, smooth white cream layer in the middle. One cookie in the center is broken to show the creamy filling inside, which looks fluffy and slightly melting. The cookies rest on a white marbled surface. photo taken with an iphone --ar 2:3 --v 7

Step 1: Whisking Your Dry Spices and Flour

Start by combining your flour with the ginger, cinnamon, nutmeg, cloves, baking soda, baking powder, and salt. I like to whisk them together really well to distribute those spices evenly — it makes every bite consistently flavorful. Take your time here; even mixing pays off.

Step 2: Mixing Wet Ingredients and Combining

Next, whisk molasses into hot water (just off the boil) and let it cool slightly so the egg doesn’t cook when added. Then stir in sugar and oil, and finally beat in the room-temperature egg. When mixing wet into dry, fold gently but thoroughly with a spatula or use a mixer on medium speed. The batter is heavy and oily-looking — that’s normal! Don't mix too little or you'll end up with patches of flour, but don’t overmix or it’ll get tough.

Step 3: Chill The Dough To Perfection

Cover and refrigerate your dough for at least two hours, though overnight is wonderful if you have time. Chilling solidifies the oil and lets flavors deepen. Trust me, skipping this step will affect the texture and flavor.

Step 4: Scoop, Bake, and Cool

When you’re ready, preheat the oven to 350°F (177°C) and line your pans with parchment or silicone mats. Use a tablespoon or cookie scoop to drop mounds of dough spaced well apart. Bake for about 13-14 minutes — edges will look set, tops may still be soft. Let cool on the baking sheet briefly before transferring to a rack to avoid breakage.

Step 5: Whip Up That Cream Cheese Filling

Beat softened cream cheese until silky smooth, then add butter and beat again until combined. Slowly mix in sifted confectioners’ sugar, vanilla, and a pinch of the same spices from the cookies. Give it a taste—adjust spices if needed for that perfect warm sweetness with a hint of tang.

Step 6: Assemble and Enjoy

Pair up cookies by size, then spread or pipe the filling evenly on the flat side of one cookie before sandwiching it with its partner. I like to use a piping bag with a Wilton 1A tip for neatness, but a small spatula works great too. Refrigerate to set or dig in right away!

Top Tip

Over the years I’ve learned a few tricks that really elevate this Gingerbread Whoopie Pies with Cream Cheese Filling Recipe, making it foolproof and extra delicious. Here are some tips I wish I’d known from the start:

Chill the dough thoroughly: Don’t rush this—chilling firms up the batter, making baking easier and improving the texture.
Use room temperature eggs and cream cheese: This helps ingredients blend smoothly so you don’t end up with lumps or tough batter.
Don’t overbake: Gingerbread whoopie pies should stay soft and cakey, so pull them from the oven when edges are set but centers are still soft.
Pipe the filling for neat sandwiches: Using a piping bag lets you portion the filling evenly and avoid a mess, but spreading works just fine too!

How to Serve Gingerbread Whoopie Pies with Cream Cheese Filling Recipe

gingerbread whoopie pies - Serving Suggestion

Garnishes

I like to garnish freshly assembled whoopie pies with a light dusting of powdered sugar or a sprinkle of finely chopped crystallized ginger for a little zing and a festive look. Sometimes a drizzle of melted dark chocolate makes them truly special—perfect if you want to wow guests.

Side Dishes

These are perfect with a warm cup of chai tea or spiced hot cocoa. For a holiday brunch, I serve them alongside fresh fruit salad or a simple bowl of mixed nuts—adds a nice balance to all that sweetness.

Creative Ways to Present

I’ve wrapped individual whoopie pies in clear cellophane tied with ribbon for gifting, which is always a hit. Or pile them on a tiered tray with pine sprigs and cinnamon sticks for a festive party centerpiece that invites everyone to help themselves.

Make Ahead and Storage

Storing Leftovers

Once assembled, cover your Gingerbread Whoopie Pies tightly with plastic wrap or pop them in an airtight container and store in the fridge — they’ll stay fresh and delicious up to one week. I even find that letting them sit overnight enhances the flavors, making them even better the next day.

Freezing

I’ve had great success freezing both the whoopie pie cookies and the fully assembled pies. Wrap each sandwich snugly in plastic wrap then place in a freezer-safe container. They freeze beautifully for up to three months. When you want one, just thaw overnight in the fridge or at room temperature.

Reheating

If you want to enjoy them warm, I gently microwave a whoopie pie (after unwrapping) for about 10 seconds. This softens the filling and cookie, though I usually eat them chilled because the flavors really shine through fully.

Frequently Asked Questions:

Can I use blackstrap molasses instead of dark molasses?

Blackstrap molasses is much more bitter than unsulphured or dark molasses and can overpower the flavors in this recipe. I recommend sticking with dark or unsulphured molasses for the best balance of sweetness and depth.

How long can I store the whoopie pies with cream cheese filling?

Once assembled, you can refrigerate the whoopie pies for up to one week in an airtight container. This keeps the filling fresh and the cookies soft. For longer storage, freezing is an excellent option.

Can I make the filling ahead of time?

Absolutely! The cream cheese filling can be made up to two days in advance and kept covered in the refrigerator. Just give it a quick stir before assembling the pies to maintain its smooth texture.

Do I need to bring the dough to room temperature before baking?

No need to bring the dough to room temperature. You can scoop and bake the gingerbread whoopie pies straight from the refrigerator. This actually helps the cookies hold their shape better while baking.

Final Thoughts

This Gingerbread Whoopie Pies with Cream Cheese Filling Recipe truly feels like a warm, cozy secret I love sharing. The way the vibrant spices flirt with rich molasses and creamy filling makes it a timeless treat. Whether it’s a special occasion or just an ordinary day, baking these always fills my kitchen—and my heart—with pure joy. I hope you enjoy making and sharing them as much as I do!