Human-induced environmental change and fishing pressure have deleterious effects on marine ecosystems, but beyond that, the longer-term impacts are much harder to assess. Here, we applied bulk nitrogen isotopes ( δ 15 N Bulk ) and compound-specific isotope analysis of amino acids ( δ 15 N AA ) to well-dated cod remains from northeast Scotland to provide insights into the trophic structure in the North Sea over the last 1500 years. Ontogenetic changes were observable in trophic δ 15 N AA and δ 15 N trophic-source proxies but not in δ 15 N Bulk , questioning the latter’s use for inferring trophic level changes. We deployed a Bayesian generalized additive model, incorporating size-related uncertainties, to show that the trophic level of cod remained relatively stable from 500 CE to 1800 CE despite major climate and economic transitions. However, in the last 200 years, the δ 15 N trophic-source proxy increased against the expectations of the effects of overfishing. While an increase in the trophic level of cod may be attributable to a restructuring of the North Sea food web owing to overfishing, other variables such as stress and diet quality might have affected nitrogen isotope fractionation, leading to similar outcomes. Our results show that multiple factors could drive δ 15 N through time; thus, physiological and biochemical factors must be considered when evaluating long-term trophic dynamics. This article is part of the theme issue ‘Shifting seas: understanding deep-time human impacts on marine ecosystems’.