Staphylococcal food poisoning is one of the most prevalent causes of foodborne intoxication worldwide. Sandwiches and desserts are susceptible to contamination by S. aureus due to the high proportion of manual work during their production. Our study aimed to evaluate the impact of storage conditions on staphylococcal enterotoxin production in sandwiches and buttercream puffs. Foods were inoculated with different S. aureus strains capable of producing type A, B, and C staphylococcal enterotoxins and incubated at 15, 25, and 30 °C. During the storage, samples were analysed for S. aureus counts and for staphylococcal enterotoxins. An enzyme-linked fluorescence assay was used to detect staphylococcal enterotoxins. The influence of inappropriate storage on S. aureus growth and staphylococcal enterotoxin production was evaluated. No staphylococcal enterotoxins were detected in sandwiches stored for 72 h at any of the tested temperatures. In buttercream puffs, enterotoxins type A, B, and C were detected within 24 h of storage at 25 °C.