Objective We analyze the processing sequence involved in the manufacture of a skull-cup and the manipulation of human bones from the Early Neolithic of Cueva de El Toro (Malaga, Spain). Materials and methods The Early Neolithic material studied includes human remains found in two separate assemblages. Assemblage A consists of one skull-cup, a non-manipulated adult human mandible, and four ceramic vessels. Assemblage B contains manipulated and non-manipulated human remains that appeared mingled with domestic waste. Using a taphonomic approach, we evaluate the skull-cup processing and the anthropogenic alteration of human bones. Results The skull-cup was processed by careful paring away of skin, fragmentation of the facial skeleton and base of the skull, and controlled percussion of the edges of the calotte to achieve a regular shape. It was later boiled for some time in a container that caused pot polish in a specific area. The other human bones appeared scattered throughout the living area, mixed with other remains of domestic activity. Some of these bones show cut marks, percussion damage for marrow extraction, and tooth/chewing marks. Discussion Evidence from Cueva de El Toro suggests that cannibalism was conducted in the domestic sphere, likely following ritualized practices where the skull-cup could have played a part. Interpretation of this evidence suggests two hypotheses: (a) aggressive cannibalism relates to extreme inter-group violence; and (b) funerary cannibalism is a facet of multi-stage burial practices. Similar evidence has been found in other Neolithic sites of this region and suggests that cannibalism and skull-cups were elements widespread in these communities. These practices may be linked to significant transformations associated with the end of the Early Neolithic in southern Iberia.