Trace element analysis of sediments from archaeological sites is a valuable method to investigate the anthropic impact and obtain information on the functions of different areas and changes in human activities. One of the most used and effective techniques to carry out this kind of analysis is inductively coupled plasma–mass spectrometry. This technique needs a previous dissolution of the sample by acid attack, but the development of the best method is still a discussed issue. In the present work, total and partial digestion methods were carried out in sediment samples of Cueva de la Cocina (Dos Aguas, Spain), and trace elements were measured and statistically compared. Major elements, soil organic matter amount, and pH data were used to evaluate the main drivers of trace element contents. The differences between the results from the two methods were highlighted. Total digestion is more effective for aluminosilicates and heavy minerals, although the partial digestion results suggested that, in most cases, the difference between the two methods is irrelevant for archaeological interpretations. Furthermore, in some cases, the total digestion of the mineral phases related to the geological contribution could mask the anthropic elemental signals.