Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a large mixing bowl, sift together the all-purpose flour, unsweetened cocoa powder, granulated sugar, baking soda, and salt.
In a separate bowl, whisk together the almond milk, vegetable oil, white vinegar, and vanilla extract until well combined.
Pour the wet ingredients into the dry ingredients and stir gently with a spatula until just combined. Do not overmix; the batter will be thick.
Fold in the semi-sweet chocolate chips evenly throughout the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out with a few moist crumbs.
Remove the muffins from the oven and allow them to cool in the tin for 5 minutes.
Transfer the muffins to a wire rack to cool completely before serving.