Heat 1 1/2 tbsp of almond milk in a narrow, microwave-safe dish in the microwave for 15-25 seconds or until it just starts to boil. Add chocolate chips and stir to melt. Set aside to cool slightly.
Add frozen yogurt, protein powder, pudding mix, almond milk, marshmallow extract, and ice cubes to a blender. Blend until smooth.
Angle a tall glass and drizzle chocolate ganache along the sides of the glass. Pour protein shake into the glass and top with crushed graham cracker and whipped cream, if desired.