Prepare Chia Pudding: In a bowl, mix the chia seeds, almond milk, maple syrup, and vanilla extract until well combined. Allow the mixture to sit for 5 minutes, then stir again to prevent any clumping. Cover and refrigerate for at least 2 hours, or overnight, until it thickens into a pudding consistency.
Prepare Blueberry-Yogurt Mix: Blend half of the blueberries into the vegan yogurt. Blend until it has reached your desired consistency.
Assemble the Puddings: Start with a layer of the blueberry yogurt mixture at the bottom of each cup, followed by a layer of chia pudding. Finish with a topping of fresh blueberries.