Preheat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a large mixing bowl, whisk together the all-purpose flour, granulated sugar, baking powder, baking soda, and salt until well combined.
In a separate medium bowl, combine the unsweetened almond milk, vegetable oil, apple cider vinegar, and vanilla extract. Stir until blended.
Pour the wet ingredients into the dry ingredients and gently fold together using a spatula until just combined. Do not overmix; some lumps are okay.
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 clean or 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.