Abstract Size-based indicators are important tools for understanding how environmental variability and fishing impact on marine populations and communities. Ideally, they would standardise fishery-independent survey data. However, this is not possible in many of the world's ecosystems with important commercial fisheries. Using fishery-dependent data we investigated changes in the size–structure of pelagic catches off Northern Chile and whether or not these changes are influenced by the environment. We computed single- and multispecies, size-based fishery indicators (SBFIs) from 1990 to 2008 for the main commercial species, anchovy (Engraulis ringens), sardine (Sardinops sagax), jack mackerel (Trachurus murphyi) and mackerel (Scomber japonicus). SBFIs indicated a downward trend of body size in the catches taking all species together; a decrease of large sardine, an increase of small jack mackerel together with a decrease of larger sizes. Anchovy remained stable in body size and catch per unit of effort over the time period. Significant effects of the environment on mean length and catch per unit of effort were found for anchovy and sardine, respectively. We conclude that catches of pelagic species have shifted to smaller body sizes, with anchovy becoming the dominant species in the catches. We discuss the changes in the context of simultaneous, long-term, climate variability and fishing mortality.