The highly productive upwelling environment off Peru sustains one of the world's largest fisheries, the Peruvian anchoveta (Engraulis ringens), but biomass variability on interannual to decadal timescales results in dramatic catch variations. In order to infer decadal- to centennial-scale variability in pelagic fish populations, we quantified variations in fish scale abundance preserved in laminated sediments collected in the Oxygen Minimum Zone off Pisco, Peru. Sediment redox conditions were reconstructed using Molybdenum while productivity was inferred from total organic carbon. Given the complex sedimentation patterns, we reconstructed a composite record from four box-cores, which was dated using ²¹⁰Pb, ²⁴¹Am and ¹⁴C. The composite record allows the identification of three marked periods. From ~1550 to ~1820, low abundance and higher degradation of fish scales, in combination with lower productivity and oxidizing conditions characterized the record. A multi-decadal period, from ~1820 to ~1890, is characterized by the presence of oceanic waters species and strong variability in redox conditions and productivity. Finally, from ~1890 to the present, a centennial-scale increase of anchovy scales is supported by high productivity and reducing conditions. Various modes of variability with regards to the relative abundances of anchovy and sardine can be observed in the Humboldt Current Ecosystem.