Beach protection and monitoring has been used for about half a century to multiple rookeries globally as an effective sea turtle conservation strategy with successful population recovery at some. Loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) turtles nesting in South Africa have been continuously protected and monitored since 1963, representing one of the longest running sea turtle beach monitoring programs in the world (>54 years). Evidence suggests that these previously harvested populations are growing, as illustrated by increased numbers of nesting females and proportion of new recruits in the nesting cohort. A 35-year time series of consistently conducted nesting beach survey was used to assess trends in female sizes over time for both species. Despite increased nesting numbers, a significant 3.7 and 3.6 cm decrease in the size of both recruit and remigrant female loggerhead turtles, but a stable mean size of leatherbacks for both age groups is observed. We hypothesize that these contradictory effects are attributable to the very distinct foraging ecologies of the two turtle species and speculate that the variation in carapace length may be driven by environmental change. Further research is needed to examine the impacts of a decreased or increased female turtle size on reproductive outputs and overall population growth. The trends observed in this study emphasize the importance of long-term monitoring, examining not only abundance, but also individual size, to understand population dynamics and support recovery planning and conservation practices.