Preheat the oven to 350 degrees F (175 degrees C). Line 18 muffin cups with paper liners.
Combine flour, sugar, cocoa, baking soda, and salt for cupcakes together in a bowl. Add water, oil, vinegar, and vanilla and beat until combined; be careful not to overmix.
Beat vegan cream cheese and sugar for filling together in a separate bowl until smooth. Add vegan yogurt, cornstarch, vanilla, and salt and beat until combined. Fold in chocolate chips.
Fill each prepared muffin cup 2/3 full with chocolate batter. Spoon a heaping tablespoon of the cream cheese mixture on top of the chocolate batter. Sprinkle the remaining sugar on top.
Bake in the preheated oven until both the cake and filling appear set, about 20 minutes. Remove from the oven and let cool completely, about 30 minutes; these taste best when completely cooled.
Nutritional Facts
Per 18 servings
Calories: 247
Carbohydrate: 34g
Fat: 14g
Fiber: 4g
Protein: 3g
Sugar: 16g
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