Ichnological analysis of Eocene deep-pelagic whitish chalky calcilutites interstratified with high-energy calcarenite beds in the lower part of the Petra Tou Romiou section (southern Cyprus) was conducted to interpret the development and evolution of the trace maker associations during calcilutite deposition after high-energy episodes. The trace fossil assemblage from the chalky calcilutites consists of Chondrites isp. (Chondrites intricatus and Chondrites targionii), Planolites isp., Taenidium isp., Thalassinoides isp., and Zoophycos isp., typical of the Zoophycos ichnofacies. A composite chalky ichnofabric reveals a multi-tiered association of burrowing animals: the uppermost tier determines a mottled background, the upper tier shows the highest trace fossil abundance and diversity (Planolites, Taenidium and Thalassinoides), the middle tier features Zoophycos and large Chondrites, and the deepest tier consists mainly/exclusively of small Chondrites. This ichnofabric has an autocomposite character, associated with bioturbation by a single ichnocoenosis and gradual upward migration of the tiered macrobenthic community as the pelagic calcilutite sedimentation slowly progresses. There are no changes in the trace fossil assemblage between or within calcilutite intervals, regardless of the associated calcarenite beds. This supports a stable, mature, background calcilutite trace maker association, which recovers shortly after the deposition of high-energy calcarenites. In turn, there would have been a rapid re-establishment of paleoenvironmental conditions during pelagic calcilutite accumulation after episodic deposition of any calcarenitic material.