The trace-fossil name Tubotomaculum has been extensively used to refer to spindle-shaped pellet-filled tubes present in Upper Cretaceous to Miocene deep-marine deposits of the western Mediterranean region. However, it has never been formally diagnosed, and accordingly it was regarded as a nomen nudum. In this paper, we formally introduce the ichnogenus Tubotomaculum, including the new ichnospecies Tubotomaculum mediterranensis. Bioglyphs, represented by scratch traces that may be present on the basal and lateral surfaces of the structure, suggesting production by crustaceans. The functional meaning of these structures challenges the simple model of a mining strategy. Instead, the storing of pellets to use them as a bacteria-enriched resource during times when organic detritus was scarce is suggested. The association with chemoautothrophic bacteria in modern analogs of Tubotomaculum provides a crucial piece of evidence to support the cache model. Integration of information from modern environments and the fossil record points to a connection between Tubotomaculum, mud volcanism, fluid venting, and hydrocarbon seeps. The presence of bioglyphs suggests firmgrounds that may have resulted from bottom current scouring of the sea sediment, leading to erosional exhumation of previously buried compacted sediment, which was therefore available for colonization by the infauna. However, an alternative scenario involves enriched fluids related to mud-volcanism resulting in reducing conditions that favored carbonate precipitation and nodule formation just a few centimeters below the sediment-water interface.