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1. Preheat oven to 350 degrees and grease pans or line with cupcake liners.
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2. In a large bowl, combine flour, sugar, cocoa powder, baking soda and salt.
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3. In a small bowl, combine yogurt, applesauce, oil, almond milk, egg and vanilla extract.
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4. Pour the wet ingredients into the dry and stir just until combined.
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5. Add 3/4 cup of the chocolate chips and stir.
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6. Fill mini muffin tins 3/4 full and sprinkle with the remaining chocolate chips. Bake for 8-14 minutes depending on the mini muffin size (there's two different sizes that the pans come in). If making regular sized muffins, bake for 16-22 minutes!
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7. Serve warm or cold!