The New Zealand geoduck clam is a unique seafood delicacy, with animals selling for up to $US 220–330/kg. Stress accumulated during transport of juveniles to grow-out sites represent a bottleneck in the aquaculture process. In this study, the physiological responses of juvenile geoducks following emersion (3- and 8-h), and recovery (1- and 5-days) were investigated. An integrated approach of flow cytometry, osmolality and metabolomics, along with behavioural assessments was used. Both cellular and chemical haemolymph parameters and metabolite profiles were recorded for P. zelandica juveniles and are reported herein for the first time. An increase in haemolymph osmolality was experienced with an increase in emersion period, with significant differences seen between the 3- and 8-h emersion groups after 5 days of recovery. Viability measures of haemocytes varied insignificantly between experimental groups, creating baseline ranges. The proportion of haemocytes undergoing respiratory burst activity did not appear to be affected by emersion and re-immersion. Haemocyte mitochondrial membrane potential was highest following 1-day of recovery, likely linked to metabolic readjustment, and increased glycolysis, taking place following emersion. Metabolomics analyses suggest that protein, lipid and carbohydrate metabolite classes assist with energy production in geoducks. Activation of anaerobic metabolic pathways, with a high dependence on succinate, were prominent in the 8-h exposure group, with metabolic recovery still taking place following 5-days of immersion, mainly due to proteins restoring energy reserves. Elucidating the physiological responses of juvenile geoduck subjected to transport stress can aid cultivation methods already underway to develop a novel, high value aquaculture industry.