Small pelagics are suitable candidates to identify regime shifts in fish stocks. They respond rapidly to ocean climate changes, specifically with a fast growth and early maturation in warm waters. This work examines landings data of small pelagics over a 40-year period (1980-2019), and auction and laboratory data of two species (Scomber colias and Trachurus picturatus) from Madeira (NE Atlantic Ocean). Integrated data on Sea Surface Temperature Anomaly (SSTA) and North Atlantic Oscillation (NAO) is also discussed. General Additive Models (GAMs) showed that a regime shift occurred in 2002, within a 2000-2003 transition period. SSTA and NAO data explained up to 88.2% of the community shift. Temperature-driven changes are not limited to a decrease of landings but also to a low gonadosomatic index (GSI) and first maturity size, as well as an increase in natural mortality of both species. This trend was relentless despite the implemented stock management actions. An urgent need to consider ocean warming in the management of fish stocks is required.