These gluten free Salted Caramel Cheesecake Cupcakes can be made small enough to fit in a spoon, or slightly larger for a reasonable size portion. You can use the tips in this recipe to make any cheesecake recipe gluten free. This one is for cheesecake lovers!
Serve these at the end of a big meal like a traditional gluten free turkey dinner or gluten free charcuterie board party. With a little effort on the presentation these are worthy of any special occasion.
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Ingredients
To make a gluten free crumb crust I used Kinnikinnick brand graham style crumbs or the crackers crushed by you. The Canadian brand Kinnikinnick gluten-free has been around for decades, ships internationally and offers a discount for larger orders.
- gluten free graham style cracker crumbs
- butter
- cream cheese
- quinoa flour (or sweet rice flour)
- eggs
- sour cream
- whipping cream
- caramel sauce
- sea salt flakes
See recipe for exact amounts and complete ingredient list.
Substitutions
Quinoa flour - Cheesecake recipes typically contain a small amount of wheat flour to properly set the cheese filling. The best way to find your favourite gluten free flour substitute is to bake.
I’ve used both sweet rice flour and quinoa flour in this recipe. Quinoa flour sets the filling more firmly when making a large cheesecake. With these mini cupcakes I found both sweet rice flour and quinoa flour were successful substitutes.
Feel free to experibake with other flours and eat your way to success.
Tips for Baking with Quinoa Flour
Here are two points to know if you've not used quinoa flour yet. First, not everyone can tolerate quinoa. Second, the odd taste you may notice (if you lick the filling off the beaters) disappears when the cheesecake is cooked.
To learn more about this flour check out my post, How To Use Quinoa Flour in gluten free baking.
Easy Caramel Sauce
Caramel sauce should be naturally gluten free (famous last words) and can readily be purchased. Savvy label readers often wonder what all the other ingredients on the label are for and move toward making many sauces at home.
The ingredients are likely already in your kitchen and you'll be rewarded with deliciousness so that might just make it worth the effort. It will last in the back of the fridge for months, but only days when it’s at the front in plain view.
Caramel Sauce vs Butterscotch Sauce
As an everyday home cook I never put too much thought into the difference between caramel and butterscotch. It is something I don’t often make yet it’s delicious enough to put in a jar and give as a gift.

Real caramel sauce is made by caramelizing sugar over very low heat. This requires a little skill and some patience so is not for everyone.
That means my easy caramel sauce recipe is actually butterscotch, oops. But as I like to remind my readers, in your kitchen you can rename every recipe you make to suit yourself.
Does Sea Salt Make a Difference
Yes! For both sweet and savoury dishes use good quality sea salt flakes. If you haven't tried it yet my personal favourite is Maldon sea salt flakes.
The finishing touch to these Salted Caramel Cheesecake Cupcakes is a few flakes of sea salt. There is a wide variety of specialty sea salts available. They come in a many textures and colours, each with their own distinct flavour from trace minerals.
In case the thought crossed your mind; no, you cannot use table salt in place of sea salt. Just don't try it!
Get The Tools
Every kitchen needs a few tools. Buy the ones you like and expect most of them to last a very long time.
- 12-count mini-muffin tins for cheesecake cupcakes and so much more.
- KITCHEN TIP: Put cooked cupcakes into a second cupcake liner to show off the colourful paper cupcake liners. It’s worth keeping a small supply on hand.
- silicone cupcake liners are the best environmental choice and ideal for everyday muffins and cupcakes.
- Portion scoops make the job of filling the paper liners easy and also ensures a consistent size for more even baking.
- The cupcake corer is a fun tool for more serious cupcake bakers.
- For people who like to take their cupcakes to the party, cupcake takers come in a variety of shapes and sizes.
- At home you can display cupcakes on any flat tray or a pedestal tray. Regular size cupcakes can be displayed in a fancy, twirling cupcake display stand. Mine spends the vast majority of time on a shelf collecting dust but it's cute when it's full of cupcakes.
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New here? Overwhelmed or frustrated? Get started with these 29 Tips about GF flour and get cooking. I can help you learn to cook gluten free food everyone wants to eat, and have fun doing it.
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Salted Caramel Cheesecake Cupcakes
Ingredients
GRAHAM STYLE CRACKER CRUST
- 2 cups gluten free graham style cracker crumbs
- 3 tablespoon sugar
- 6 tablespoon butter, melted
CHEESECAKE FILLING
- 2 packages cream cheese , room temperature (8 oz/250g)
- ¼ cup sugar
- 1½ tablespoon quinoa flour (or sweet rice flour)
- 2 eggs
- 1 teaspoon vanilla
- ¼ cup sour cream
- ¼ cup whipping cream
SERVING
- caramel sauce
- sea salt flakes
Instructions
GRAHAM STYLE CRACKER CRUST
- Preheat oven to 350°F.
- In a large bowl combine graham cracker crumbs, sugar and melted butter. Stir until combined.
- Line mini muffin tin with paper liners. Fill each paper liner with 1 tablespoon crumb mixture. Pack firmly into pan. (I used the bottom of a liqueur glass.)
- Bake in preheated oven 5 minutes. Cool before filling.
CHEESECAKE FILLING
- In a small bowl combine sugar and flour. Set aside.
- In large bowl of a stand mixer beat cream cheese until smooth, 2 or 3 minutes.
- Add sugar/flour mixture to cream cheese and continue beating until combined.
- With motor running add eggs one at a time.
- Add vanilla, sour cream and heavy cream beating until combined.
- Pour filling over crumb crust filling almost to the top of each paper liner. They will bake with a rounded top then as they cool the filling will settle creating a small indent for the caramel topping.
- Bake in preheated oven for 12-14 minutes.
- Cool completely on baking racks. Refrigerate over night in an airtight container. Cupcakes can be kept in the fridge for several days or frozen if needed.
SERVING
- Using an espresso spoon add a dot of caramel sauce on each cupcake.
- Just before serving sprinkle with a few flakes of salt.



















Steshni Corea
salted caramel 😍