The sequence of decay in fern pinnules was tracked using the species Davallia canariensis. Taphonomic alterations in the sediment–water interface (control tanks) and in subaqueous conditions with microbial mats were compared. The decay sequences were similar in control and mat tanks; in both cases, pinnules preserved the shape throughout the four-month experience. However, the quality and integrity of tissues were greater in mats. In control tanks, in which we detected anoxic and neutral acid conditions, the appearance of a fungal–bacterial biofilm promoted mechanical (cell breakage and tissue distortions) and geochemical changes (infrequent mineralizations) on the external and internal pinnule tissues. In mats, characterized by stable dissolved oxygen and basic pH, pinnules became progressively entombed. These settings, together with the products derived from mat metabolisms (exopolymeric substances, proteins, and rich-Ca nucleation), promoted the integrity of external and internal tissues, and favored massive and diverse mineralization processes. The experience validates that the patterns of taphonomic alterations may be applied in fossil plants.