Gluten Free Salted Caramel Cheesecake Cupcakes



This recipe is for cheesecake lovers. Delicious on its’ own, cheesecake lends itself to all kinds of variations and in this case I created tiny Salted Caramel Cheesecake Cupcakes.

With a little effort on the presentation these are worthy of any special occasion. I served some cupcakes on fancy serving spoons and placed the rest on small mirrors. For those of you who prefer a deliciously messy dessert try drizzling the caramel sauce back and forth over an entire tray of cheesecake cupcakes, sprinkle with salt and invite everyone to dig in.

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To make a gluten free crumb crust for these cheesecake cupcakes I used Kinnikinnick graham style crumbs. I added a dab of caramel sauce and a sprinkling of sea salt flakes to turn them from regular cheesecake into amazing Salted Caramel Cheesecake Cupcakes!

Cheesecake recipes typically contain a small amount of wheat flour that can successfully be substituted with a gluten free flour. I’ve used both sweet rice flour and quinoa flour in cheesecake but I haven’t experimented beyond that. Feel free to experibake with other flours and eat your way to discovering a favourite.

Gluten Free Flour Substitutes

Much has been written about all the different gluten free flour options. For anyone new to quinoa flour there is one important point to note, specifically to those who will lick the beaters or run your finger through the batter for a taste test. Before quinoa flour is baked it has an odd taste. This taste completely disappears when baked so there is nothing to worry about. Your final cheesecake will taste like any cheesecake you have ever tasted.

To learn more about quinoa flour you can check out my post; How To Use Almond Flour and Quinoa Flour.

Caramel Sauce vs Butterscotch Sauce

Caramel sauce should be naturally gluten free and can easily be purchased anywhere. During the pandemic we are all ‘staying home’ more so it’s a good time to learn just how easy it is to make. This would be a great school project for any age!

As an everyday home cook I never put too much thought into the difference between caramel and butterscotch. It is something I don’t make often 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 and so it requires a little skill and some patience. This is not for everyone. That means my 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.

This caramel sauce will last in the back of the fridge for months, but only days if it’s in plain view.

PIN for later…

Salted Caramel Cheesecake Cupcakes on decorative spoons.

Sea Salt

“Salt is what makes things taste bad when it isn’t in them.”


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. Salt is essential in cooking and is primarily used for flavour and texture. To use on both sweet or savoury dishes I suggest you purchase a good quality sea salt. My personal favourite Maldon sea salt flakes.

In case the thought crossed your mind; no, you cannot use table salt.

Get The Tools – Cupcakes

Every kitchen needs a few tools. Buy the ones you like and expect most of them to last a very long time.

  • 6 or 12-count regular size muffin tins or12-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.
  • Both reusable piping bags or disposable piping bags (12, 24 or 50 count boxes) are easy to use. If you don’t have them a regular zipper type bag works for icing anything. The quality of a freezer bag is less likely to blow up on you.
  • 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.

This recipe was inspired by the photo of Salted Caramel Cheesecake Bars I saw over at Cupcakes OMG. 

I’d love to hear in the comments below if you made these and how you presented them.

This recipe was originally posted October 2015, updated April 2020.

More Cupcake and Caramel Recipes


2 cups GF graham style cracker crumbs
3 Tbsp sugar
6 Tbsp butter, melted
2 - 8 oz/250g packages cream cheese, room temperature
¼ cup sugar
1½ Tbsp sweet rice flour or quinoa flour
2 eggs
1 tsp vanilla
¼ cup sour cream
¼ cup whipping cream
caramel sauce and sea salt flakes


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 Tbsp crumb mixture. Pack firmly into pan. (I used the bottom of a liqueur glass.)
Bake in preheated oven 5 minutes. Cool before 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.
Using an espresso spoon add a dot of caramel sauce on each cupcake.
Just before serving sprinkle with a few flakes of salt.

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