Mini Cheesecakes Gluten-Free

Featured in Sweet Treats and Baked Favorites.

Learn how to whip up smooth gluten-free mini cheesecakes using a muffin tin. These rich, handheld desserts combine a creamy filling on a buttery graham crust. No tricky techniques are required—just basic tools like liners and readily available ingredients. Bake them until set, chill, then serve plain or dress them up with whipped cream, tangy lemon curd, fresh fruit, or even chocolate. They’re freezer-friendly, easy to customize, and always a hit for group events!

Aisha
Updated on Thu, 08 May 2025 01:22:27 GMT
Dessert plate with cream and berries. Pin it
Dessert plate with cream and berries. | cookingflavor.com

I've completely changed my dessert approach with these fancy gluten-free mini cheesecakes. They've got this amazing creamy filling on top of a rich, buttery graham cracker base that gives you all the wow factor of regular cheesecake but in cute little single servings.

My next-door neighbor tried these at our block party last summer and right away asked how to make them. Now whenever we have friends over for dinner, everyone wants these little treats.

  • Gluten-free graham crackers: They make a snap-worthy foundation that stands up nicely to the smooth filling
  • Cream cheese: Gives you that classic tangy flavor - don't skimp with low-fat versions
  • Sour cream: Brings extra creaminess and cuts the sweetness just right
  • Eggs: They help everything set up with that true cheesecake feel
  • Vanilla extract: Adds depth and warmth - go for the real stuff
  • Lemon juice: Wakes up all the flavors without making it taste like lemon
  • Brown sugar: Gives the crust a hint of caramel that works really well with the crackers

Detailed Cooking Guide

Get The Base Ready:
Crush gluten-free graham crackers into tiny bits. Stir in melted butter and brown sugar until it looks like damp sand. This creates a base that won't fall apart when pressed into the cupcake liners. Use about 1½ tablespoons for each cup and flatten with a glass bottom for even layers.
Whip Up The Filling:
Beat softened cream cheese until it's light and smooth, taking about 2 minutes. The cream cheese must be soft or you'll fight with lumps that won't go away. Add in sour cream, eggs, sugar, vanilla, and lemon juice, mixing slowly to keep air out which can make cracks. You want it runny and silky.
Cook Just Right:
Fill each liner almost to the top using a greased cookie scoop for less mess. Bake at 350°F for 20 minutes until the sides look set but the middle still wobbles slightly. They'll puff up while baking but sink a bit as they cool, making a nice spot for toppings. Don't leave them in too long or they'll turn out dry.
Let Them Rest:
Cool them down at room temperature before putting them in the fridge for at least 3 hours, but overnight works better. This wait is crucial for the right taste and texture to develop. You'll get that perfect creamy bite that's worth waiting for.
A plate of desserts with berries and blueberries. Pin it
A plate of desserts with berries and blueberries. | cookingflavor.com

I now swear by Schär Honeygrams for this recipe. I found them after trying to make my own gluten-free crusts that always broke apart. These crackers give you that real graham taste that makes these mini cheesecakes taste just like ones from fancy bakeries.

Fantastic Do-Ahead Treat

These little cheesecakes actually taste better when made a day early. The flavors get deeper and the texture turns even creamier after sitting in the fridge overnight. That's why they're so great for parties - you can do all the work beforehand. Just keep them covered in the fridge without any toppings until about half an hour before you serve them.

Fun Topping Suggestions

What's so great about these mini cheesecakes is how you can top them with almost anything. Fresh berries add nice color and natural sweetness. A bit of lemon curd brings a zingy tang that works well against the rich cake. Chocolate ganache turns them into something extra special. For parties, why not set out different toppings and let everyone fix their own unique dessert?

Fixing Common Problems

Even good bakers run into issues with cheesecake sometimes. If the tops crack, don't stress about it. They usually close up on their own as they cool down. For bigger cracks, just add some whipped cream or fruit on top and nobody will know. If they sink too much in the middle, they probably needed more time in the oven. Next time, bake them for another minute or two.

A plate of desserts with berries and cream. Pin it
A plate of desserts with berries and cream. | cookingflavor.com

Frequently Asked Questions

→ How do I make a gluten-free crust?

Use crushed gluten-free graham crackers, like Schär Honeygrams, mixed with melted butter and brown sugar. Press the mix firmly into cupcake liners to create a solid base.

→ What toppings go well on them?

You can’t go wrong with options like fresh fruit, whipped cream, caramel drizzle, lemon curd, chocolate syrup, or even cherry pie filling. Pick and choose your favorite!

→ Can I prepare them in advance?

Absolutely, they store great. Let them cool fully before refrigerating in a covered container. Add toppings only when ready to serve.

→ Is it okay to freeze them?

Sure thing! Keep them plain (no toppings) and store in an airtight container in the freezer for up to a month. Let them thaw in the fridge overnight or on the counter for a few minutes before serving.

→ Why do they sometimes crack?

It’s usually from baking, but it’s nothing to worry about. As they cool, the cracks tend to close. Mixing with room-temp ingredients often helps prevent cracks too.

Mini Cheesecakes Gluten-Free

Velvety gluten-free bites with graham crust.

Prep Time
10 Minutes
Cook Time
20 Minutes
Total Time
30 Minutes
By: Aicha

Category: Desserts

Difficulty: Easy

Cuisine: American

Yield: 12 Servings (12 mini cheesecakes)

Dietary: Vegetarian, Gluten-Free

Ingredients

→ Crust

01 5 tablespoons melted butter
02 2 tablespoons packed light brown sugar
03 1 1/4 cup graham cracker crumbs (choose gluten-free like Schär Honeygrams)

→ Cheesecake Filling

04 2 large eggs, brought to room temperature
05 1/2 cup room-temp sour cream
06 1 teaspoon lemon juice
07 1/2 cup sugar
08 2 teaspoons vanilla extract (pure)
09 2 (8-ounce) blocks of cream cheese, softened to room temperature

Instructions

Step 01

Warm up your oven to 350°F (175°C). Pop cupcake liners into the slots of a 12-cup muffin tray.

Step 02

Turn the cookies into crumbs using a food processor or crush them in a sealed plastic bag by rolling over it with a pin. Blend the crumbs with melted butter and sugar. Scoop around 1 1/2 tablespoons of this crust mix into each liner and pack it down tightly.

Step 03

With a hand mixer on low-medium speed, whip the softened cream cheese for 1-2 minutes till it's nice and fluffy. Throw in the sour cream, eggs, sugar, vanilla, and lemon juice. Blend till it's creamy and smooth.

Step 04

Scoop the cheesecake mixture into liners with a greased cookie scoop. Fill each one to the top so they're nice and full.

Step 05

Slide the muffin pan into the oven and bake for about 20 minutes. When you see the tops lightly browned, pull them out. They'll puff up but will shrink once cooled.

Step 06

Let them cool completely before covering and popping into the fridge. Chill for at least 3 hours, or leave them overnight. When ready to serve, let them rest at room temp for a couple of minutes before removing them from the tray.

Step 07

You can serve them plain or dress them up with toppings you like best before digging in!

Notes

  1. Warm ingredients blend way better, so make sure everything's at room temperature.
  2. If you're short on time, dip cold ingredients in warm water for 2-3 minutes to soften them up.
  3. Don’t sweat over cracks—they’ll vanish as the cheesecakes shrink while cooling.
  4. You can prep these ahead of time and store them chilled for later.

Tools You'll Need

  • Muffin tray with 12 cups
  • Liners for cupcakes
  • Food blender or a bag and rolling pin combo to smash cookies
  • Large bowl for mixing
  • Handheld mixer
  • Cookie scoop for portioning

Allergy Information

Please check ingredients for potential allergens and consult a health professional if in doubt.
  • Has dairy products (cream cheese, sour cream, butter)
  • Contains eggs

Nutrition Facts (Per Serving)

It is important to consider this information as approximate and not to use it as definitive health advice.
  • Calories: 153
  • Total Fat: 8 g
  • Total Carbohydrate: 17 g
  • Protein: 2 g