Spaghetti squash tastes the same whether it is cooked in a microwave or an oven, according to Startcooking.com. The only noticeable difference between cooking methods is that the spaghetti squash becomes softer when using the microwave method.
To prepare the spaghetti squash for baking in the oven, lightly rub olive oil all over the flesh of the squash, and then sprinkle it with salt and pepper. This helps the flavor develop further. In the microwave, omit the olive oil, but season the squash with salt and pepper. When the squash has finished cooking, allow it to sit for five minutes before serving.