Poor nutritional condition of seed of the green-lipped mussel Perna canaliculus (Gmelin 1791) is a major cause of significant losses after seeding out onto mussel farms. Biochemical analysis of experimentally unfed seed mussels showed they preferentially depleted glycogen reserves versus lipid and protein during short periods of starvation (≤8 days). This knowledge allowed the use of a human diabetic glucose meter to assess quickly the levels of glycogen in seed mussels after they were first homogenized and then digested with α-amylase, which converted the glycogen to glucose and maltose. The assay was sensitive enough to detect significant differences between mussels that had been continuously fed (6.04 ± 0.24 (SE) mmol/L) compared with mussels that had been unfed for 4 days (1.71 ± 0.06 mmol/L) or 8 days (0.67 ± 0.02 mmol/L). These results were consistent with biochemical analysis of the actual glycogen content of the experimental groups (16.6 ± 1.8 mg/g dry mass vs. 6.2 ± 1.0 mg/g and 5.5 ± 0.7 mg/g, respectively). This novel assay has the potential for quickly assessing the nutritional quality of seed mussels, enabling the reduction of losses of seed in the mussel farming industry.