To make overnight oats, combine soy milk, oats, Shakeology, ½ apple, chia seeds, and extract in a medium bowl; mix well. Evenly divide oat mixture between 2 jars (or sealable containers). Seal jars; refrigerate overnight.
To make the crumble, combine pecans, oats, almond flour, sugar, oil, and cinnamon in a small bowl; mix well.
After refrigeration, top each jar evenly with crumble and remaining ½ apple. Store refrigerated in an airtight container for up to 24 hours.