Preheat oven to 350F. Spray a 9X9 inch baking pan with vegetable cooking spray or a thin coating of olive oil.
Heat the vegan butter over medium heat in a small sauce pan until melted, about 30 seconds. Add the flour, 1 tablespoon at a time, stirring in between. The goal is to create a thick sauce. Add salt and pepper. Stir to combine.
Add the plant-based milk, a little at a time, stirring in between. This should create a gravy-like sauce. If your sauce has lumps, simply transfer to a food processor or blender and pulse until smooth.
Remove from heat and add 1/2 cup vegan cheddar shreds. Stir until melted.
Place 1/3 of the potato slices in the bottom of prepared pan. Top with 1/3 of the the sliced onions. Pour 1/3 of the cream sauce evenly over the top of the potatoes and onions. Repeat until all the potatoes, onions, and sauce is used. Top with remaining cheese.
Cover with foil and bake in heated oven for 50 minutes. Use tongs to remove foil and bake for 10 minutes, until the edges turn a golden brown.
Remove from oven and allow to cool for 10 - 15 minutes before serving.
To store, allow scalloped potatoes to come to room temperature, then cover and refrigerate. These will keep in the fridge for up to 5 days.