Chocolate Chip Cheesecake Chocolate Cupcakes (gluten-free with vegan options)
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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.
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, Keto Snowball Cookies, and Low-carb Almond Crescents are great, but this recipe for vegan cheesecake cupcakes, well, it really takes the cake (see what I did there?)
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 mostly we eat whole grain only. So I tried to make this recipe to fit what we needed.
I saw cheesecake cupcakes made by another blogger, Ricki Heller, and I knew that I had to make them into a version that we could have.
So I went in the kitchen and got to work.
I tweaked her filling and used my Homemade Chocolate Chips with a few other alterations and they worked out great.
Creamy dairy-free cheesecake filling with crunchy chunky chocolate (or carob) chips, surrounded by a “just right” chocolate cake.
This is a “healthy” recipe, so if you use whole grains they won’t be super light and fluffy, but we like our desserts to be more hearty.
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How to Use the Extra Filling
You will have extra filling using the proportions in this recipe. I thought about reducing the proportions, but we like having the extra.
My husband likes to add it to his cupcakes by putting a big dollop on top kind of like frosting. He’s not at all a fan of frosting, but since these cupcakes are not super sweet it’s just right for him.
Our oldest just eats the filling by the spoonful for a snack.
You could, alternatively, use it as a healthy frosting or even a healthy dip.
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. 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’d like, you can swap out a little of the whole grain flour for a white flour or starch but likely they’ll still sink.
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.
- 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 should work in place of coconut oil, but I haven’t tried it. I would recommend only substituting with another oil that’s solid at room temperature.
- 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.
How to Store
I recommend storing these cupcakes in the fridge where they should keep for at least a week. You can also freeze them in a freezer-friendly container to have healthy treats at the ready anytime.
More Yummy Allergy-Free Treats
These allergy-friendly treats are great recipes to have on hand for those who are on special diets, but even those who aren’t can enjoy!
– Homemade Almond Joy
– Pumpkin Snickerdoodles
– No-Bake Coconut Delights
– Luscious Lemon Bars
Chocolate Chip Cheesecake-Filled Chocolate Vegan Cupcakes (gluten, egg, & sugar-free w/ dairy-free option)
Ingredients
Filling
- 3 cups cashews (sunflower seeds work as well)
- 9 tablespoons water
- 3/8 cup lemon juice
- 7 tablespoons low carb sweetener
- 3/16 teaspoon stevia extract (or 6 scoops)
- 4 teaspoons vanilla extract
- 3/16 teaspoon salt
- 1 cup sugar-free chocolate chips
Cake
- 4 cups gluten-free flour mix (see Recipe Notes)
- 1/2 cup arrowroot starch (or other light starch)
- 1 1/2 cups cocoa (or carob for AIP)
- 1 teaspoon gelatin (see Recipe Notes for vegan option)
- 1 tablespoon baking soda
- 1 tablespoon baking powder
- 2 2/3 cups low-carb sweetener
- 1 teaspoon salt
- 3 1/2 cups coconut milk
- 1/8 teaspoon stevia extract (or 4 scoops)
- 2 teaspoons vanilla
- 1/4 cup apple cider vinegar
- 1/2 cup coconut oil (melted)
Instructions
- 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.
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.
- Use 1/2 cup any healthy sweetener of your choice can be used instead of stevia.
- Vegans could use a gum like xanthan gum or organic guar gum instead of gelatin.
- 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.
- You can use other milk alternatives, including almond milk, instead of coconut milk.
- You can likely substitute any other fat that’s solid at room temperature for the 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.
Nutrition
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.
What’s your favorite cupcake recipe?
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.
Thanks!
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: https://wholenewmom.com/health-concerns/how-to-like-stevia/ . hope that helps and hope you like them!!
Anything I can use in place of lemon juice for the filling? Maybe orange juice concentrate? My son can’t have lemon :-/
I would think lime or maybe a little apple cider vinegar instead. Can he have lime?
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!
Sooo glad to hear that!!! My son has been begging me to make them again!