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For the cupcakes: Preheat the oven to 325 degrees F. Line standard-size cupcake pans with 16 cupcake liners.
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In a medium bowl, whisk together the soy milk, agave nectar, canola oil, cane sugar, vanilla extract and apple cider vinegar, and set aside.
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In a large bowl, sift the flour, cocoa powders, baking powder, baking soda and salt and whisk them together.
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Add your wet mixture to the dry and whisk until the mixture is evenly moist and only a few lumps remain.
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Set aside.
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For the ganache: Whisk together the chocolate chunks, soy milk and agave nectar in a microwave-safe bowl.
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Place the bowl into a microwave and heat for 1-minute increments, whisking in-between, until the mixture is thick and smooth.
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Take your cupcake batter and start to stream in about 1 cup of the chocolate ganache and gently fold it into the batter.
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Do not fully mix it into the batter, it should be swirled in.
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Fill the liners three-quarters full and bake until a toothpick comes out clean, 12 to 15 minutes.
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Cool the cupcakes completely.
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For the salted caramel sauce: In a nonstick saucepan, add the coconut milk fat.
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Add in the brown sugar, vanilla and salt, and whisk well.
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Bring the mixture to a boil on medium-high heat, whisking occasionally.
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Once the mixture starts to boil, reduce the heat to a low bowl and cook for 35 to 45 minutes, whisking every couple of minutes, until the sauce has reduced by half.
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The resulting mixture will be thick and golden.
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Allow the caramel to cool slightly and use immediately.
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For the buttercream: Whip the shortening and margarine together in a mixer bowl with the paddle attachment until fluffy.
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Scrape down the bowl and put back onto the mixer on low-speed and slowly add the powdered sugar and cocoa powder.
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Once the mixture is fully incorporated, stream in 1 cup of the chocolate ganache.
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Once the ganache is added, you may turn the mixer to medium-high and whip until the buttercream is very fluffy.
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To assemble: Poke a hole in the center of each cupcake using the end of a wooden spoon or small offset spatula.
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Fill the hole completely with salted caramel sauce.
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Using a round frosting tip, generously frost the top of each cupcake with the dark chocolate buttercream.
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Drizzle the top of each cupcake with more salted caramel sauce.