Preheat the oven to 350 degrees F (175 degrees C). Spray two 9x13-inch baking dishes with nonstick cooking spray.
Layer potatoes and onions in the prepared baking dishes, seasoning each layer with salt and pepper.
Melt non-dairy butter in a medium saucepan over medium heat. Stir in flour until blended. Whisk in vegetable broth, stirring constantly, until sauce boils and thickens. Pour sauce over the potatoes and onions; sprinkle paprika over the top.
Bake in the preheated oven until potatoes are tender and golden brown, about 50 minutes.