Skin mucus is increasingly used as a source for determining immunity-related proteins and enzymes. However, the ability to accurately measure some activities may be modified by inadequate handling and storage of the samples. This study aims to measure the effect of freezing and lyophilization at the time of collection on such activities. Fresh, frozen (immediately after collection at −20 °C and −80 °C) and lyophilized skin mucus samples obtained from the same groups of fish specimens of gilthead seabream (Sparus aurata L.) were analysed in the assays. The amount of total proteins and sugar residues (determined by lectin binding) present in skin mucus samples fell after both freezing and lyophilization of the samples. While no significant differences were exhibited in the levels of some proteins or enzymes (immunoglobulin M, antiprotease, peroxidase, esterase and alkaline phosphatase) determined in fresh or frozen mucus samples, protease and lysozyme activities were lower in frozen mucus samples than in fresh samples. Lyophilization of the mucus samples drastically decreased the total level of proteins obtained, as well as of protease, peroxidase, lysozyme and alkaline phosphatase activities. The results suggest that freezing skin mucus samples is more suitable than lyophilization if samples are stored before determining enzymatic activities.