Chocolate Chip Cheesecake Chocolate Vegan Cupcakes (gluten, egg, & sugar free w/ dairy-free option)

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Chocolate Chip Cheesecake Cupcakes that are both gluten-free and vegan? Yes, please! These Vegan Cheesecake Cupcakes are a super special treat for anyone on a special diet–a great dessert to make ahead and have on hand for special occasions throughout the year!

Chocolate Chip Vegan Cheesecake Cupcakes - Gluten Free, Sugar Free & Vegan Cupcakes that taste amazing! Delicious chocolate cupcakes filled with a dairy free cheesecake filling that's sure to please.

Though I don’t do as much gluten-free baking as I used to, I still love making healthier special treats for my family on occasion. These Pumpkin Snickerdoodles, Grain-Free Chocolate Chip Cookies, and Macaroons are some of our favorites, but this recipe for vegan cheesecake cupcakes, well–it really takes the cake :).

That’s a cupcake funny there, in case you missed it.

I used to make homemade low fat cheesecakes as a special treat for holidays. They were amazing.  But our diets have changed.

Now we eat a sugar-free diet, plus we’re dairy-free (due to my son’s life-threatening food allergies), and whole grain only.  Could I make something fabulous with those restrictions?

I typically love a culinary challenge, but this one seemed a little steep.

I saw these fabulous cupcakes by Ricki Heller (one of my favorite bloggers) and knew I had to have them.

The vegan cheesecake inside reminded me of the lovely cheesecakes I used to make and I just knew my family would love them.

So I went in the kitchen and got to work. Ricki’s recipe is already great, of course (like so many of her recipes are) but I wanted to get a way around the fruit juices in the cake part to make them less of a glycemic issue for us.

And I ended up tweaking her cheesecake filler a bit.

chocolate chip vegan cheesecake cupcakes collage

Well, we have a real winner here, folks.

These Chocolate Chip Vegan Cheesecake Cupcakes are amazing.  The 24 cupcakes I made were gone in a flash and I have 3 men (2 of them are pretty young) begging for more.

(By the way–not a follower of Ricki’s?  Hop on over there and check out her wonderful blog now :-).)

Anyway, I paired the tweaked “cheesecake” filling with my Homemade Chocolate Chips and a recipe from a site called Copycat Cook (that no longer exists) with a few minor alterations.

The result?


More On these Vegan Cheesecake Cupcakes

  • Please use Soaked and Dehydrated Nuts or Seeds.
  • If you use a stronger-tasting nut or seed like pumpkin seeds, you will need more sweetener.  (Pumpkin seeds are a great zinc source, by the way.)  Macadamias and cashews are a good mild choice for this filling.
  • I used a minimal amount of starch because I try to bake with whole grain flours only.  The cupcakes sink “a tad” using this recipe.  If you want a completely “non sinking” cupcake, trade a little of the whole grain flour for some starch.
chocolate chip vegan cheesecake cupcakes

Recipe Notes

  • My basic “go to” gluten-free flour blend is typically 4 parts sweet brown rice, 4 parts mixed whole grain gluten-free flours, consisting of millet, buckwheat, amaranth, and long grain brown rice.  I pretty much use whatever I have on hand :-).
  • Macadamias will work just as well as cashews, and if needed, you can substitute any nut or seed.
  • Here is a great brand of stevia scoops. Also see this post for more help with stevia. 1/2 cup any healthy sweetener of your choice can be used instead of stevia.
  • See my Homemade Chocolate Chips if you would like to make your own chocolate chips.
  • Vegans could use a gum like xanthan gum or organic guar gum instead of gelatin.
  • Read this recipe for making your own baking powder.
  • Any healthy sweetener can be substituted for the xylitol. I use xylitol since it is a low-glycemic sweetener, but there are lots of other sweeteners that are low glycemic. See this post for help with substituting sweeteners.
  • You can use other milk alternatives, including almond milk, instead of coconut milk. See these recipes for coconut milk and almond milk. Of course, dairy milk can be used as well.
  • Any other healthy oil can be used in place of coconut oil.
  • Grain-free Option: This recipe should work with a grain-free / low-carb flour like almond flour by increasing the baking powder by 50% and reducing the coconut oil by half. I haven’t tried it yet but I think it should work.
  • AIP: This would be a tough recipe to make AIP but you could try it by making an AIP cream cheese and using a cassava flour blend and of course using carob instead of cocoa. I haven’t tried this but I think it would be doable.
chocolate cupcakes

Chocolate Chip Cheesecake-Filled Chocolate Vegan Cupcakes (gluten, egg, & sugar-free w/ dairy-free option)

These Chocolate Chip Vegan Cheesecake Cupcakes are one of our favorites — gluten free and sugar free too!
Print Pin Rate
Course: Dessert, Snack
Cuisine: Dairy-Free, Gluten-Free, Vegan
Calories: 215kcal





  • Make the filling first so it has time to cool.  (If you make my Homemade Chocolate Chips with coconut oil you will want it cool or it might melt the chips :-(.)
  • Place all filling ingredients other than the chocolate chips in a high-powered blender (like a Vitamix) and blend ’til smooth.
  • Fold chocolate chips into the cheesecake mixture.
  • Make the cake batter.
  • Fill prepared muffin tins about 1/2 full with cake batter.
  • Spoon about 2 teaspoon of the cheesecake mixture on top of the cake batter.
  • Top each cupcake with remaining cake batter.
  • Bake in 350-degree oven for about 30 minutes, or until a tester comes clean out of the cupcake part.


Calories: 215kcal | Carbohydrates: 21g | Protein: 5g | Fat: 15g | Saturated Fat: 9g | Sodium: 174mg | Potassium: 213mg | Fiber: 3g | Sugar: 1g | Vitamin A: 1IU | Vitamin C: 1mg | Calcium: 37mg | Iron: 3mg | Net Carbs: 18g

Nutritional information is provided as a courtesy and is merely an approximation. Optional ingredients are not included and when there is an alternative, the primary ingredient is typically used. We cannot guarantee the accuracy of the nutritional information given for any recipe on this site. Erythritol carbs are not included in carb counts since they have been shown not to impact blood sugar. Net carbs are the total carbs minus fiber.

Creamy dairy-free cheesecake filling with crunchy chunky chocolate (or carob) chips, surrounded by a “just right” chocolate cake.

Honestly, I’ve made a number of cakes over the years (well, I do make more cookies and such than cakes), but these vegan cheesecake cupcakes were a clear favorite.

Gobbled up lickety-split.

By the way, you will have extra filling with these proportions.  I thought about reducing the proportions, but we really liked having the extra.

My husband likes to add it to his cupcakes by putting a big dollop on top when he ate them.  He’s not at all a fan of frosting, but the sweetness in this filling is just right.

My oldest just eats the filling by the spoonful for a snack :-).

Just plop some of that filling from the yummy vegan cheesecake cupcakes onto your already stuffed cupcakes and you’ve got a double layer of goodness.

You’re welcome.

You could, alternatively, use it as frosting of sorts.  Or even a fruit dip.

Whatever way you choose to eat is, it’s just great.

More Yummy Allergy-Free Treats!

Homemade Almond Joy
Pumpkin Snickerdoodles
No-Bake Coconut Delights
Luscious Lemon Bars

What’s your favorite cupcake recipe?

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  1. I really want to try these!
    I was wondering how much stevia I have to use to make up for the xylitol. Unfortunately for me my husband cannot tolerate it.

    1. Hi there. This post I can’t believe it – I just realized that somehow my payments never happened for kannaway!!! Glad i caught it! has conversion into – 1/32 tsp stevia is the same as about 2 T sugar / xylitol but I do prefer to blend / combine w/ other sweeteners as outlined in this post: . hope that helps and hope you like them!!

  2. Anything I can use in place of lemon juice for the filling? Maybe orange juice concentrate? My son can’t have lemon :-/

  3. I made these tonight for an independence day cookout with friends of my husband whom I never met until tonight. Needless to say, I was pretty bold as I took them out of the oven as we were walking out the door. I had no idea what they would taste like or even if they baked correctly. Our hostess is intoletant to both dairy and gluten, so when dessert came, I was so nervous. They were great. My husband woukd have likes them to be a little sweeter, but I enjoyed them and so did she!