Haemolymph and tissue samples of Haliotis rubra × laevigata hybrid abalone were taken during a routine stock movement procedure on an Australian abalone farm to look for biochemical and histological changes associated with anaesthesia and/or manual movement of the abalone, both of which are used in commercial stock movement operations. Sections of the left kidney, the gill and the surface of the foot were examined under light microscopy and a scoring system was used to measure observed changes and compare treatment groups to controls. The left kidney of anaesthetised abalone contained less protein and haemocytes than control or manually moved abalone on the day of anaesthesia (p < 0.05), but returned to baseline levels within 1 day. The foot muscle of anaesthetised and moved abalone had areas of denuded epithelium 5 days after anaesthesia (p < 0.05). Protein, phosphate, magnesium, sodium, chloride, calcium and potassium levels were measured in the cell-free haemolymph. The protein levels were significantly elevated compared to controls on the day after anaesthesia and manual movement (p < 0.05), but declined to baseline levels within 3 days. There were no significant differences in the other measured ions. Benzocaine anaesthesia, with or without subsequent movement, led to greater histological changes in tissues of abalone, than manual movement without anaesthetic. Comparison of physiological and histopathological changes with haemolymph immune assays may show whether the non-destructive haemolymph sampling can provide early warning of stressors that cause tissue damage. The methods used can be applied to scientifically assess any husbandry procedures with a view to improve stock management and productivity.