These tiny Salted Caramel Cheesecake Cupcakes is a recipe for cheesecake lovers. Cheesecake lends itself to all kinds of variations and this one is a winner!

Salted Caramel Cheesecake Cupcakes served on fancy spoons with colourful beaded handles.

With a little effort on the presentation these are worthy of any special occasion. I served them on fancy serving spoons and placed the rest on small mirrors to create an inviting display.

For those of you who prefer a deliciously messy dessert drizzle caramel sauce back and forth over an entire tray of cheesecake cupcakes, sprinkle with salt and invite everyone to dig in.

Gluten Free Crumb Crust

To make a gluten free crumb crust I used Kinnikinnick brand graham style crumbs. There are more than a few brands readily available so check your stores. The Canadian brand Kinnikinnick has been around for decades, ships internationally and offers a discount for larger orders.

Gluten Free Flour Substitutes for Cheesecake

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 cheesecake. 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 discovering a favourite. I haven't experimented beyond these two flours because, you know, I can only eat so much cheesecake.

Pros and Cons of Quinoa Flour

I have a separate post on How To Use Almond Flour and Quinoa Flour if you want to learn all the details.

Here I simply want to highlight two points. First, not everyone can tolerate quinoa. Secondly, the odd taste you may notice if you lick the filling off the beaters will disappear when the cheesecake is cooked. Whew!

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.

A jar of Homemade Caramel Sauce wrapped and labelled for a gift; beside a sauce boat with caramel sauce on a ladle dripping back into the dish.

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

“Salt is what makes things taste bad when it isn’t in them.”
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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 good quality sea salt flakes, it really does make a difference. My personal favourite is Maldon sea salt flakes.

In case the thought crossed your mind; no, you cannot use table salt in a recipe like this.

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.

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.

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