Whisk almond milk, yogurt, 2 tbsp maple syrup, vanilla, 1 tsp cinnamon, and salt in a bowl.
Stir in chia seeds. Rest 10 minutes, then stir again. Cover and chill 30 minutes or overnight.
Warm a skillet over medium heat. Add apples, lemon juice, water, 1 tbsp maple syrup, 1 tsp cinnamon, and nutmeg.
Cook, stirring, until tender and glossy, 6–8 minutes. Set aside to cool slightly.
Toast oats and nuts in a clean skillet over medium heat, 2–3 minutes, until fragrant.
Stir in almond flour and coconut oil with a pinch of salt. Cook until lightly golden, 3–4 minutes. Cool to crisp.
Assemble cups: spoon chia pudding, top with warm apples, then scatter crumble.
Serve right away or chill for later.