High-resolution benthic and planktonic stable oxygen isotope records are presented for the upper Miocene Ain el Beida (AEB) section in northwestern Morocco and reveal the clear imprint of the (climatic) precession, obliquity, and eccentricity cycles in the interval between 6.5 and 5.5 Ma. The δ¹⁸O depth series were transformed into time series using astronomical tuning of the sedimentary color cycles to the 65°N summer insolation curve of the La93 solution with present-day values for tidal dissipation and dynamical ellipticity. Spectral analysis and band-pass filtering show that the ratios of the astronomically related spectral peaks are not consistent in the depth and time domain. The inconsistencies are mainly due to variations in sedimentation rate that are positively correlated with precession amplitude (i.e., modulated by eccentricity). In addition, they result from a long-term trend in sedimentation rate. A simple model of nonlinear response of the sedimentation rate to the eccentricity modulation of precession was used to simulate the observed shifts in the relative position of the spectral peaks in the depth domain. Cross-spectral analysis was carried out on the δ¹⁸O time series and a combined eccentricity, tilt (obliquity), and precession (ETP) curve. The precession-controlled δ¹⁸O signal varies in-phase with ETP partly as a result of the tuning procedure, while the obliquity related signal reveals a small lag of 2–3 kyr relative to obliquity. This lag is slightly reduced at the time of the Messinian Salinity Crisis (MSC) and increases to 5–6 kyr if the tidal dissipation term in the astronomical solution is reduced to half its present-day value. The obliquity-related lag is most likely associated with the slow buildup of ice caps, whereas the precession signal is interpreted as to dominantly reflect regional climate changes comparable to those associated with Mediterranean sapropels. Finally, the benthic δ¹⁸O record is compared with open ocean records and discussed in terms of an astronomically tuned oxygen isotope stratigraphic framework.