Integration of geochronological analyses of in situ zircons with the petrological study of their microstructural growth microdomains (through petrography and phase diagram modeling) yields a more precise interpretation and understanding of any geological process than the study of ages from separate zircons. This is essential especially for those rocks affected by polymetamorphic histories. We present new in situ U-Pb zircon dating from metapelitic granulites exposed in the contact with the ultramafic massif of Beni Bousera (northern Morocco, Western Mediterranean). Geochronological data scatter from Paleoproterozoic (1508 ± 23 Ma) to Miocene (22.9 ± 0.7 Ma), though the majority of ages range between 100 and 400 Ma, with four main peak ages clustering around 390–319, 286–264, 193, and 105 Ma. The Middle Permian (ca. 286–264 Ma) and earliest Miocene (22.9 ± 0.7 Ma) ages are constrained from a thermobarometric point of view: The former ages represent the formation of the zircons at depth (higher pressure), and the latter ages represent the exhumation process (lower pressure). Combining these petrological results with previous geophysical and geodynamical studies from the literature in the area, we propose a four-step geodynamic model for the Beni Bousera orogenic peridotite since the end of the Paleozoic (i.e., Middle Permian) to the present, supporting an evolution linked to a subduction-related scenario since Late Cretaceous times.