Abstract Interactions between cetaceans and the purse seine fishery in coastal waters of mainland Portugal were investigated using onboard observations over a period of 15 years (2003–2018). In 10% of the fishing sets, there were interactions with one of three species of cetaceans: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), and harbour porpoise (Phocoena phocoena). The common dolphin was the most frequently observed species, occurring in 89% of all interaction events, and the only species with observed mortality. Therefore, this study focused only on the interactions with common dolphins. A generalized additive model (GAM) was applied to observer data to investigate how the fishing activity and the abundance of small pelagic fish influenced the probability of occurrence of interactions between the common dolphin and the purse seine fishery between 2003 and 2018. The results revealed significant annual and geographic variation in the occurrence of interactions, and a significant influence of fishing effort and catch per unit effort of sardine (Sardina pilchardus). A second GAM in a hurdle model was used to model the number of common dolphins that interacted with the fishing activity as a function of fishing seasonality and the local abundance of pelagic fish. There was a significant effect of the seasonality of the fishing activity and catch per unit effort of sardine and chub mackerel (Scomber colias) on the number of common dolphins interacting with the fishery. The results of this study suggest that the probability of interactions and the number of common dolphins interacting with the fishery were affected by the local abundance of sardine and chub mackerel. As the common dolphin population appears to be increasing in the study area, the risk of by‐catch also increases, thus the monitoring of the Portuguese purse seine fishery is important to inform the implementation of management plans, and also as a response to global efforts for sustainable fisheries and marine mammal conservation.