In an attempt to assess trends of Holocene sea-surface temperature (SST), two proxies have been compiled and analyzed in light of model simulations. The data reveal contrasting SST trends, depending upon the proxy used to derive Holocene SST history. To reconcile these mismatches between proxies in the estimated Holocene SST trends, it has been proposed that the Holocene evolution of orbitally-driven seasonality of the incoming radiation is the first-order driving mechanism of the observed SST trends. Such hypothesis has been further tested in numerical models of the Earth system with important implications for SST signals ultimately recorded by marine sediment cores. The analysis of model results and alkenone proxy data for the Holocene indicate a similar pattern in temperature change, but the simulated SST trends underestimate the proxy-based SST trends by a factor of two to five. SST trends based on Mg/Ca show no correspondence with model results. We explore whether the consideration of different growing seasons and depth habitats of the planktonic organisms used for temperature reconstruction could lead to a better agreement of model results with alkenone data on a regional scale. We found that invoking shifts in the living season and habitat depth can remove some of the model–data discrepancies in SST trends. Our results indicate that modeled and reconstructed temperature trends are to a large degree only qualitatively comparable, thus providing at present a challenge for the interpretation of proxy data as well as the model sensitivity to orbital forcing.