Creamy Chocolate Filled Cupcakes

Creamy Chocolate Cupcakes-side view 01Who doesn’t like chocolate? I do and I especially love dark chocolate. These irresistible chocolate filled cupcakes with a creamy chocolate filling will satisfy your craving for chocolate. They are gluten free, vegan, and are naturally sweetened with stevia and agave nectar. They are also the best moist gluten-free chocolate filled cupcakes I’ve ever had. You would never believe there is less natural sugar in a dozen of these cupcakes than there is in a quarter of an apple from the agave nectar I put in the filling.

I love chocolate but I rarely buy any from stores. The main reason is that the high sugar content, which is usually the no food value refined sugar. The chocolate tastes more like candy than chocolate. I am glad I was able to make this healthy creamy chocolate filling with very low sugar content at home. It is sweetened from an all nature sweetener called agave nectar. I had fun experimenting with different ingredients and developing a good way to make them.

Creamy Chocolate Cupcakes-on rack

The filling is inspired from here. I omitted the sugar and condensed milk and used coconut cream instead. The filling is less runny than the original recipe but still rich and creamy and healthier. Adding a small amount of instant decaf coffee really boosted the intense chocolate flavor.

Creamy Chocolate Cupcakes-filling

Making a soft, moist, and light spongy gluten-free chocolate cake is something I’ve been thinking about for a long time. I found a perfect recipe from  and converted it to a no-sugar-added version. I replaced sugar with unsweetened applesauce and pure stevia extract powder. The addition of applesauce gives extra moisture to the cake. It also provides additional acidity to react with baking soda and perfectly balances the taste. Baking soda, white vinegar, and applesauce are the keys to make the cake spongy and fluffy with many air holes.

Creamy Chocolate Filled Cupcakes-muffin cups

We served our son, Leo, his favorite fruit, grapes, while we were enjoying these incredible cupcakes. He immediately dropped his grapes and pointed at the cupcakes. Yes, we got his message. After he had a small piece, he made the same crescendoing mmmm groan just like his dad did. I hope you will enjoy these healthy, guilt free cupcakes as much as we will this holiday season.

Creamy Chocolate Cupcakes-top view


Creamy Chocolate Filled Cupcakes
Prep Time
1 hr 30 mins
Cook Time
18 mins
Total Time
1 hr 48 mins
Tools: Fine mesh strainer, measuring cups and spoons, mixing bowls, egg whisk, food processor, spatula, 12-cup regular size muffin pan.
Servings: 12 regular size
Creamy Chocolate Fillings
  • ¾ cup unsweetened coconut cream
  • ¼ cup coconut oil
  • ½ cup cocoa powder
  • 1 tbs agave nectar
  • 1/8 tsp pure stevia extract powder
  • 1 tsp vanilla extract
  • pinch of salt
  • 1 tbs instant decafe coffee
Cupcake Batter (Dry)
  • 42 g 1.48 oz brown rice flour
  • 42 g 1.48 oz millet flour
  • 42 g 1.48 oz white rice flour
  • 42 g 1.48 oz sweet rice flour
  • 21 g 0.74 oz potato starch
  • 10 g 0.35 oz corn starch
  • 11 g 0.39 oz tapioca starch
  • ½ cup unsweetened cocoa powder
  • ¼ tsp salt
  • 1 tsp baking soda
  • ¼ tsp pure stevia extract
Cupcake Batter (Wet)
  • 1 cup apple sauce
  • 1 tsp vanilla extract
  • ½ tbs distilled white vinegar
  • 1/3 cup canola oil
  • ¼ cup water
  • optional 1 tbs unsweetened shredded coconut (finely grounded)
  1. Use a fine mesh strainer to sift the cocoa powder over a mixing bowl. Whisk all chocolate filling ingredients together and then pour the mixture into a plate. Place the container in freezer for 15 minutes.
  2. Take the chocolate filling mixture out from freezer. The mixture should be somewhat solid but soft to work with. The coconut oil will be slightly separated from the mixture. Transfer the filling mixture into a food processor. Blend the mixture together briefly.
  3. Scoop out approximately 1 tbs of the filling mixture at a time and then roll it into a ball. It will yield about 12 balls.
  4. Place the balls back on the plate; cover with plastic wrap or other cover and return it back to freezer to chill for at least 1 hour.
  5. Preheat the oven to 350 °F. Lightly spray the muffin cups with vegetable oil spray or butter (use vegan butter if desired).
  6. Sift and whisk all dry ingredients together in a mixing bowl. Set aside.
  7. Whisk all wet ingredients together in another mixing bowl. Mix the dry ingredients into the wet mixture and stir until just combined.
  8. Scoop out approximately 1 tbs of the cake batter and place it on the bottom of the prepared muffin cups. Place one chocolate ball into each muffin cup. Fill the muffin cup with more cake batter, making sure the chocolate balls are surrounded and covered with cake batter.
  9. Bake for 18 minutes until the cupcakes are springy. Let them cool in the pan for 5 minutes, then carefully transfer to a wire cooling rack. Serve warm.
  10. (Optional) Dust the top of cupcakes with finely ground coconut.
Recipe Notes

1. This recipe can also be made from the commercial all-purpose gluten-free flour.
2. I usually make a large batch of this gluten free flour mix because you can weigh large amounts of each ingredient more accurately than small amounts. The extra flour mix can be stored in a ziploc bag in the freezer.


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