Although roots and tubers are dietary staples in many parts of the world, their use is difficult to document archaeologically because their organic remains are often poorly preserved in archaeological sediments. Here we describe the first diagnostic phytoliths from the underground storage organs of the important New World agricultural crops manioc or yuca (Manihot esculenta Crantz), arrowroot (Maranta arundinacea L.), and llerén (Calathea allouia [Aubl.] Lindl.) and demonstrate their usefulness for identifying prehistoric root and tuber processing with a study of stone artifacts from a Valdivia 3 (2800–2400 B.C., calibrated) household at Real Alto, Ecuador. Gelatinized starch (heat-altered) and unaltered starch from maize (Zea mays L.), arrowroot, and manioc were also found on these stone tools. Our data document early evidence for manioc in Ecuador's coastal lowlands. In combination, these phytoliths and starch residues provide evidence that both raw and cooked foods were processed in this early mixed agricultural economy.