In general, it is best to remove the seeds from cucumber before using them in a recipe. Although the cucumber seeds and skin are entirely edible, the seeds contain unwanted moisture which can lead to a soggy dish, or add unwanted texture. Plus, the seeds sometimes contain a bitter flavor that can overpower the flavor of the recipe. However, you can choose to leave the seeds if you are eating the dish right away, and if their taste does not bother you, as they are highly nutritious.