Pumpkin seeds are a rich source of nutrients, including protein, fiber, healthy fats, and minerals like magnesium and phosphorus. Pepitas, or shelled pumpkin seeds: If you find the texture of whole pumpkin seeds too tough, you might prefer shelled pumpkin seeds, also called pepitas. Pumpkin seeds have also been studied for their possible roles in fighting cancer, neurodegenerative diseases, and type 2 diabetes. How To Prepare ThemWhile whole pumpkin seeds can be found at grocery stores, you can also scoop them out of a fresh pumpkin. Pumpkin seeds last different amounts of time depending on whether they’re store-bought or fresh from a pumpkin.