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The Best Keto Apple Caramel Cheesecake Cups | THM-S | Low Carb

These rich, delicious keto apple caramel cheesecake cups are served up in shot glasses. Serve them as part of a dessert buffet or as the perfect way to end a fall dinner party.

Is there anything more perfect for a fall dessert than caramel apples?

Okay, maybe something with pumpkin.

But caramel and apples is one of my favorite combinations!

As soon as I made these Salted Caramel Cheesecake desserts, I knew they would be amazing with some apple added in.

Shot glasses filled with keto caramel apple cheesecake parfaits on a wood board next to whole red apples

I made a few tweaks to the cheesecake base to reduce the fat just a little bit.

But don’t worry, these miniature cheesecake parfaits are still wonderfully decadent!

The recipe below uses low carb sweeteners so these desserts only have 5 net carbs each.

Don’t worry if you still eat sugar, though, I’ve included how to make this recipe with sugar in the notes of the printable recipe at the end of this post.

Woman holding a shot glass filled with caramel apple cheesecake parfait and a tiny plastic spoon

I love that miniature desserts like these help me with portion control.

These keto cheesecake shooters are so rich, that a little bit goes a long way!

So even on days that I may want a bigger serving, I’ll stick to just the one.

Closeup of a shot glass filled with low carb caramel apple cheesecake parfait

They also look kind of fancy so you can serve them to company for dessert.

Everyone will think you spent hours!

But they’re actually very simple to make.

Miniature desserts like these are also fun to serve as part of a dessert buffet.

Then your guests get to try a variety of sweet treats.

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Can You Have Apples and Stay Keto?

Can you have apples on a keto diet?

The short answer is generally no.

Even a small apple has 20 grams of carbs, and they’re likely to throw you out of ketosis.


Diced apples on a wood cutting board

This recipe divides a small apple into eight servings.

That means each serving only has 2.5 carbs from the apple.

If you are prone to blood sugar spikes, you can omit the apples and use one of the substitutes below.

Be sure to dice the apples into tiny chunks, about 1/4-inch cubes, so you can easily divide them into two layers in the small glasses.

What Are Keto Alternatives for Apples?

You have a couple of options if you choose to omit the apples from this recipe.

  1. Use zucchini, yellow squash, or chayote squash instead of the apples. These have a similar texture to apples when cooked. Be sure to only use the fleshy part of the squash and omit the part with the seeds. Add 1 teaspoon of apple extract to the mixture for flavor.
  2. Skip the apple layer, and add 1 tsp of apple extract to the cheesecake layer.

How to Make Caramelized Apples

Whether you use apple, zucchini, yellow squash, or chayote squash, the method is the same.

Stainless steel saucepan with diced apples that have cooked down to a pie filling

Add all the ingredients for the filling to a heavy saucepan and simmer until the apples (or squash) are fork tender.

Continue simmering until the liquid evaporates and the sauce becomes more like caramel.

It’s important to use the right low carb sweetener for the apples!

Allulose is the best option because it won’t crystallize.

If you aren’t counting carbs, you can use an equal amount of granulated sugar.

The Best Way to Make Keto Caramel Sauce

Caramel is one of those things that was challenging to make keto-friendly and have the right texture.

Most low-carb sweeteners tend to crystallize when they cool.

Enter allulose.

This is the first keto-friendly sweetener I’ve found that stays silky and creamy, even after it’s cooled!

There are a few tricks to making a perfect sugar-free caramel sauce.

First, always use a pan with a thick bottom like a stainless steel saucepan with a thick bottom, or a heavy duty nonstick skillet.

If the pan is too thin, the sauce may end up burning before it thickens.

Start by melting the butter, then add the allulose.

And get your whisk ready…

Whisk continuously until the allulose is completely incorporated and the edges begin to simmer.

This is not one of those recipes where you can stop whisking while the pan is over the heat!

Don’t worry, it only takes about 2 minutes.

Once the sauce is completely smooth and simmering, you can take a little break from the whisking if you want to.

Small stainless steel saucepan with homemade keto caramel sauce and a whisk

Let the low carb caramel sauce simmer, whisking every 15-30 seconds until it turns a light golden brown.

Be sure to watch it carefully because if it turns too brown then it’s burnt and you’ll have to start all over.

And clean up a smelly mess from your pan.

Seriously, do not step away because it browns to the right point very quickly!

Personally, I like to just keep stirring until it turns this shade of brown.

Small stainless saucepan on a gas stove with boiling homemade caramel sauce being whisked

Keep the sauce over the heat and add the whipping cream while whisking.

It’s going to bubble up a lot.

Just keep on whisking for approximately 30-60 seconds until the bubbling slows down.

Remove the sauce from the heat and stir in the vanilla extract and salt.

Then let the sauce cool while you assemble the cheesecake mixture.

The sauce will get thicker as it cools.

You can also make the sauce ahead and refrigerate it until you’re ready to use it.

How to Perfectly Toast Nuts

Toasting the pecans adds so much flavor to them!

Or rather, it intensifies their flavor.

Since our portions are small, getting the most flavor possible really makes a difference.

Saute pan with finely chopped toasting pecans being stirred with a wood spoon on a gas stove

Add 1 teaspoon of butter to a saute pan along with the finely chopped pecans and cinnamon.

Heat the nuts over medium heat, stirring every few minutes.

You can easily do this while you’re making the caramel sauce or the apple filling.

While you want to keep an eye on them, they aren’t as finicky as the caramel sauce!

Just give them a stir and when they start smelling good, you’re about done.

Don’t toast them for too much longer after they become arromatic or they may burn.

How to Easily Fill Shot Glasses with Dessert Fillings

The trick to getting the cheesecake mixture into the shot glasses without making a mess is to use a pastry bag or plastic zip-close bag.

You can use a decorative pastry tip if you want, but it’s not necessary.

If you’re using a zip-close plastic bag, cut one of the bottom corners off, being careful to not make the hole too big.

About 1/4-1/2-inch off the corner is just right.

If you want to make the layers in advance before assembling the apple caramel cheesecake parfaits, wait to cut the corner of the bag.

Then you can store the filling in the refrigerator inside the bag

Now here’s my trick for filling the bag!

Large ziploc bag folded over edges of glass mixing bowl with cheesecake filling in the bag

Place the bag inside of a tall glass or mixing bowl and turn the opening of the bag inside-out over the top edge.

This keeps the bag open so you can spoon the cheesecake filling into the bag without making a mess.

Then simply seal the top of the bag once you’ve added all the filling and you’re ready to go!

How to Assemble Individual Dessert Parfaits in a Shot Glass

Once you have the keto apple caramel cheesecake filling in the bag, it’s super easy to put this dessert together.

Get the rest of the layers together: toasted chopped pecans, keto apple pie filling, and keto caramel sauce.

I like to use actual measuring spoons to get the same amount of each layer into each glass.

Start with 1 teaspoon of the chopped toasted pecans.

Next, pipe in the caramel cheesecake filling.

I usually make the first layer of cheesecake about 1/3 of the glass.

Tap the glass or use a small spoon to smoosh the filling down.

Drizzle a scant teaspoon of caramel sauce into the glass.

Now add the sugar-free apple pie filling, and then another teaspoon of the chopped pecans.

Top with a second layer of the cheesecake filling.

Divide the remaining cheesecake as evenly as possible between the 8 glasses.

Don’t worry if they look kind of full!

Tap the glasses to help everything settle and add 1/2 teaspoon of the pecans.

Then drizzle another teaspoon of caramel sauce and divide the remaining apples over top.

Shot glasses filled with keto caramel apple cheesecake parfaits on a wood board with thin apple slice garnishes

Ideas for Garnishing These No-Bake Cheesecake Parfaits

I like to keep the garnish pretty simple, but there are lots of delicious ways to top a caramel apple cheesecake parfait.

Just be sure to wait to add your garnish until you’re ready to serve them.

You’ll likely have about three teaspoons of chopped pecans left after assembling the mini parfait cups. These are great as a garnish because they’ll stay crunchy on top.

Some other garnishes to try:

  • thin slices of apple
  • shaved chocolate
  • crushed sugar free toffee
  • sprinkle of cinnamon, nutmeg, or apple pie spice
  • tiny mint leaf
  • whipped cream
Closeup of a shot glass filled with low carb caramel apple cheesecake parfaits

Can You Make This Keto Caramel Cheesecake Dessert Ahead?

The caramel sauce can be made a week or two beforehand and stored in the fridge.

The cheesecake base can also be made as much as a week in advance and refrigerated, but it may need to be stirred prior to use.

You can even assemble these miniature desserts 3 days ahead!

The pecan layers will get a little soft and loose their crunch, but the flavor is still incredible.

Always wait to add your garnish until right before serving.

More Decadent Keto Dessert Recipes

Be sure to leave a star rating and review after you make the recipe!

This helps other people to find and enjoy it too.

Plus it means the world to us!

Shot glasses filled with keto caramel apple cheesecake parfaits on a wood board with thin apple slice garnishes

Keto Apple Caramel Cheesecake Parfait Cups

Yield: 8
Prep Time: 45 minutes

These rich, delicious keto apple caramel cheesecake cups are served up in shot glasses. Serve them as part of a dessert buffet or as the perfect way to end a fall dinner party. Refer to the Notes for substitutions.


Toasted Pecans

  • 6 T chopped pecans
  • 1/4 tsp ground cinnamon
  • 1 tsp butter

Apple Filling

  • 1 small gala apple (1-1/4 cup diced)****
  • 1/2 tsp apple pie spice
  • 1/8 tsp salt
  • 2 Tbsp allulose*
  • 2 Tbsp water

Caramel Sauce

  • 2 Tbsp butter
  • 1/4 cup allulose*
  • 3 T heavy cream
  • 1 tsp vanilla extract
  • 1/4 tsp salt

Caramel Cheesecake

  • 8 oz. neufchatel cheese, sof
  • 1/2 cup Fage plain nonfat Greek yogurt**
  • 1/4 cup Swerve brown (or to taste)
  • 1 tsp vanilla extract


Caramel Sauce

  1. Melt the butter in a thick-bottomed saucepan or a nonstick skillet over medium heat. Add the allulose* and whisk continuously until the sweetener is completely incorporated. The sauce will become creamy and smooth but it takes a little longer than with sugar. Keep whisking until it's completely smooth!
  2. Once the sauce is smooth, let it simmer, whisking every 15-30 seconds until it turns a light golden brown, approximately 2 minutes. Watch it carefully! If it turns too brown then it's burnt.
  3. Add the whipping cream while whisking. It will bubble up a lot, but keep on whisking for approximately 30-60 seconds.
  4. Remove the sauce from the heat and stir in the vanilla extract and salt. Let the sauce cool while you assemble the cheesecake mixture. You can make the sauce ahead and refrigerate it until you're ready to use it.

Apple Pie Filling

  1. In a small saucepan, combine diced apple (see notes for substitution), apple pie spice, salt, allulose, and water. Bring to a boil over medium hat.
  2. Simmer the apples until they're fork tender and the sauce has reduced and is caramelized.
  3. Remove from heat and let the mixture cool. Can be made ahead and refrigerated until you're ready to assemble.

Toasted Pecans

  1. In a saute pan, combine chopped pecans, cinnamon, and 1 tsp. butter. Heat over medium heat, stirring frequently, until the pecans are fragrant and lightly browned.
  2. Remove from heat and cool.

Cheesecake Filling

  1. In a mixing bowl, stir together the softened cream cheese, Fage yogurt, Swerve brown, and vanilla extract until smooth.
  2. Cut the corner off of a zip-close plastic bag. If desired, insert a decorative pastry tip in the hole (be sure to not make the hole in the bag too big!). Place the bag inside of a large glass and turn the opening of the bag inside-out over the glass to make filling the bag easier. Spoon the cheesecake filling into the bag. Seal the bag to pipe the filling into the shot glasses.

Assemble the Shooters

  1. Use 8 tall shot glasses like the ones linked below. Sprinkle 1 teaspoon of toasted pecans in the bottom of each glass.
  2. Pipe the cheesecake mixture into the bottom half of each glass. Drizzle with 1 teaspoon of caramel sauce. Sprinkle with 1 teaspoon of the toasted pecans. Add 1 teaspoon of the apples. Repeat.
  3. Serve immediately or refrigerate for up to 48 hours in a sealed container so no refrigerator aromas affect the dessert.


*Allulose: this is the best sweetener for caramel because it will not crystallize when it cools. You can use other low carb sweeteners but the sauce will not be silky smooth.

**Fage Yogurt: Fage Greek yogurt is strained more than other brands giving it a thicker texture. Other brands of Greek yogurt will "weep" and the cheesecake layer may get watery if you let it sit overnight before serving.

*** To make this recipe using sugar, use the same amounts listed for each ingredient. Substitute brown sugar for the Swerve Brown and granulated white sugar for the allulose.

**** You can substitute an equal amount of diced zucchini or chayote squash for the apple. Be sure to use the fleshy part of the zucchini and not the seedy area in the center. Add one teaspoon of apple extract for flavor.

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Nutrition Information
Yield 8 Serving Size 1
Amount Per Serving Calories 190Total Fat 16gSaturated Fat 8gTrans Fat 0gUnsaturated Fat 7gCholesterol 34mgSodium 244mgCarbohydrates 5gFiber 1gSugar 4gProtein 4.5g

Please note that we are not medical or nutritional professionals. We include nutrition information for our recipes as a courtesy to our readers. However, due to wide variations in brands, nutrition data is subject to change for every user. Nutrition data is calculated using My Fitness Pal Pro. All sugar alcohols are subtracted from the final carb count. Please refer to our complete Nutritional Disclosure for more details.

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