The dramatic decline of European eel ( Anguilla anguilla ) populations over recent decades has attracted considerable attention and concern. Furthermore, little is known about the sensitivity of the early stages of eels to projected future environmental change. Here, we investigated, for the first time, the potential combined effects of ocean warming (OW; Δ + 4°C; 18°C) and acidification (OA; Δ − 0.4 pH units) on the survival and migratory behaviour of A. anguilla glass eels, namely their preference towards riverine cues (freshwater and geosmin). Recently arrived individuals were exposed to isolated and combined OW and OA conditions for 100 days, adjusting for the salinity gradients associated with upstream migration. A two-choice test was used to investigate migratory activity and shifts in preference towards freshwater environments. While OW decreased survival and increased migratory activity, OA appears to hinder migratory response, reducing the preference for riverine cues. Our results suggest that future conditions could potentially favour an early settlement of glass eels, reducing the proportion of fully migratory individuals. Further research into the effects of climate change on eel migration and habitat selection is needed to implement efficient conservation plans for this critically endangered species.