The dependence of skeletal alteration on time spent in the taphonomic active zone (TAZ) can generate a taphonomic clock, which can be used to quantify scales of time averaging and rates of skeletal production and recycling in the fossil record. However, the strength of the taphonomic clock is variable in present-day shallow marine environments and it is unclear how this strength varies with depth. Here, we assess the strength of the taphonomic clock in Nautilus macromphalus dead shells that were collected in cool-water, sediment-starved, epi- and mesobathyal environments off New Caledonia and range in postmortem age from few decades to several millennia. We find that, first, differences in the onset and extent of alteration states in the epibathyal zone (< 750 m) segregate well-preserved shells with red stripes (less than ∼ 200 years) from encrusted shells with faded colors and extensively bored by sponges (∼ 400 years), and from strongly fragmented, bored, and coated shell relicts (> 1,000 years). The onset of dissolution and formation of clay-goethitic coating occurs earlier (∼ 200 years) in the mesobathyal zone (> 750 m) than in the epibathyal zone. Clay-goethitic rims and boring infills show signs of microbial binding, pelletization, and coccolith dissolution and can represent nascent stages of glauconitization. Second, shells several centuries old show differences between right and left flanks (1) in the degree of encrustation and sponge bioerosion in the epibathyal zone and (2) in the extent of clay-goethitic coating in the mesobathyal zone. The upper flanks are ultimately removed in both depth zones, leaving relict half-shells that are millennia old. Third, the depth dependence of alteration can reflect a bathymetric decline in disintegration rates by heterotrophic borers due to a reduced productivity in the mesobathyal zone and an increase in dissolution rates due to the proximity of the aragonite compensation depth. The between-flank asymmetry in preservation implies (1) horizontal position of shells close to the sediment-water interface for several decades or centuries without being overturned or subjected to reworking and (2) shell exposure to two distinct taphonomic regimes separated by few centimeters, with the upper flank located in the TAZ and the lower flank facing a less aggressive sediment zone. The stable exposure of shells in the taphonomic active zone and slow alteration rates in bathyal environments allow discriminating between within-habitat time-averaged assemblages on one hand and environmentally or stratigraphically condensed assemblages on the other hand.