Abstract High-resolution physical, chemical and biological-based climate proxies from the Ain el Beida (AEB) section in Atlantic Morocco reveal the imprint of the three main orbital parameters precession (19–23 kyr), obliquity (41 kyr) and eccentricity (95–125 and 400 kyr) between 6.5 and 5.5 million years before present (Ma). The precession-related variations are most prominently reflected in the color reflectance and chemical composition of the sediment, showing that precession minimum configurations lead to more humid climate conditions in Northwest Africa probably related to the Atlantic system, while more arid climate conditions prevailed during precession maxima. In addition, precession-bound changes in planktonic foraminifera and calcareous nannofossil assemblages indicate that sea surface temperature (SST) increased during the humid phases, while productivity conditions increased during the dry periods. The clear imprint of the short and long-term eccentricity cycles is explained by a non-linear climatic response to the precession forcing with overall more humid climate conditions during eccentricity maxima. The obliquity-controlled variations in SST and aridity conditions concur with glacial–interglacial variability that is conspicuously recorded in both planktonic and benthic δ 18O records of AEB. The observed warm and wet climates during interglacial periods most likely reflect the direct ice driven thermal response to the reduced ice sheets and more active Atlantic depressions. Similar as during the Pliocene and Pleistocene, obliquity-controlled variations in the planktonic and benthic carbon isotope (δ 13C) records of AEB are inversely related to the oxygen isotope records with more depleted values during glacial stages, although with a small lag. The close correspondence between the δ 13C records of AEB and other open ocean sites (i.e., Sites 982 and 926) may therefore point to large-scale glacial-controlled variations in the deep-sea carbon reservoir. Superimposed on the orbital variations, the imprint of the – onset of the – Messinian Salinity Crisis can be traced by a marked ~ 1.0‰ negative excursion in planktonic δ 13C at 6.0 Ma, followed by a prominent peak in Ti/Al at ~ 5.97 Ma.