A 50-year-long (1958–2008) historical simulation of a climate-to-fish ecosystem model for anchovy (Eugralis encrasicolus) and sardine (Sardina pilchardus) populations in the upwelling ecosystem off NW Africa is revisited and analyzed. Anchovy and sardine annual adult abundances were correlated at interannual and decadal time scales in the historical run. A three-step analysis method applied unraveled the environmental and life stage-specific drivers underlying the bottom-up mechanisms responsible for the simulated variability in anchovy and sardine populations. Changes in anchovy adult abundance were primarily controlled by larval survival, prey availability, and local upwelling strength, whereas sardine adult abundance was controlled by age-1 growth affecting age-2 fecundity and egg production via prey availability. Despite different diet preferences, the common sensitivity of anchovy and sardine to prey availability had a synchronizing effect on the two populations, with both anchovy and sardine doing better during years of higher plankton biomass and colder ocean temperatures. Analysis of potential links with modes of climate variability showed that anchovy dynamics were more tightly connected to the AMO while sardine dynamics were correlated to the NAO. This difference stemmed from the vulnerability of the anchovy population to enhanced coastal upwelling causing increased larval drift mortality. Finally, based on an earlier, similar modeling study for the Californian anchovy and Pacific sardine, we argue that the relatively warmer habitat off NW Africa compared to the coastal region off central California is a key feature explaining synchronous populations in the Canary Current versus out-of-phase anchovy and sardine cycles in the California Current.