The New Zealand's Greenshell™ mussel (Perna canaliculus) aquaculture industry is being affected by summer mortality events associated with increasing seawater temperatures and pathogens. In this study, challenge experiments were conducted to investigate, for the first time, the effects of pathogen coinfection on the survivability and haemolymph immune responses of juvenile and adult mussels. Animals were injected with marine broth (control), Vibrio mediterranei, Photobacterium swingsii, or a mixture of V. mediterranei and P. swingsii. Then, mussel survival was monitored for 72 h, and haemolymph was sampled for bacterial quantification and metabolomics analyses at 24- and 48-h post challenge. Coinfected adults and juveniles showed 100% mortality. Bacterial colony counts in haemolymph decreased as infection time continued, especially in juveniles. The haemolymph metabolome of mussels exposed to single bacterial species and coinfection showed response changes largely within energy metabolism. Mussels infected with V. mediterranei exhibited increased metabolites linked to the glutathione pathway, branched-chain amino acids, and others over time, supporting structural functions. Conversely, mussels infected with P. swingsii showed no metabolic differences over time. The coinfection group exhibited large decreases in important metabolites, such as fatty acids as an alternative energy source and amino acids to support immune functions and protein synthesis.