Mollusc shell is built up by secretion from the mantle and is the result of a controlled biological process termed biomineralisation. In general mollusc shells are well characterised however, the molecular mechanisms used by molluscs to produce shell remain largely unknown. One tractable method to study molecular biomineralisation mechanisms are shell damage-repair experiments, which stimulate calcification pathways. The present study used the Antarctic clam (Laternula elliptica) as a model to better understand when and where molecular biomineralisation events occur in the mantle. Two approaches were used: one experiment used high-throughput RNA-sequencing to study molecular damage-repair responses over a 2 month time series, and a second experiment used targeted semi-quantitative PCR to investigate the spatial location of molecular mechanisms in response to damage. Shell repair in L. elliptica was slow, lasting at least 2 months, and expression results revealed different biological processes were important at varying time scales during repair. A spatial pattern in relation to a single drilled hole was revealed for some, but not all, candidate genes suggesting the mantle may be functionally zoned and can respond to damage both locally and ubiquitously across the mantle. Valuable data on the temporal and spatial response of shell damage-repair provide a baseline not only for future studies in L. elliptica, but also other molluscs.