The identification of the mammalian species based on faecal sediments in modern and ancient environments is the aim of the research of archaeologists, forensic scientists and ecologists. Here, we set up and validated an optimized gas chromatography-mass spectrometry (GC–MS) method, characterized by a time-saving sample preparation protocol, for the simultaneous analysis of faecal biomarkers (6 sterols/stanols and 5 bile acids) in 14 soil samples from the archaeological site of “Le Colombare di Negrar” in northern Italy. Although the archaeological sediment samples examined are numerically exiguous, a comparative reading of our faecal biomarkers findings with new studies on faunal materials collected in the same stratigraphic detail during recent excavation campaigns will allow to better clarify the economic interest of the animal species farmed in the Colombare site (such as bovines, goats, sheep and pigs) and to shed light on the management of breeding. Together with archaeozoological and archaeobotanical analyses, the investigation of faecal biomarkers can increase our knowledge of how ancient local communities exploited natural resources and may allow us to deduce what their impact on the landscape was.