Our understanding of the stratigraphic expression of astronomically driven climate-change cycles in the Milankovitch frequency band has improved significantly in recent decades. However, several aspects have been little studied to date, such as the nature of the climatically regulated environmental processes that ultimately control cyclic sedimentation. Similarly, relatively little is known about the expression of Milankovitch cycles in successions accumulated in tectonically active basins. In order to fill this knowledge gap, the Albian hemipelagic deposits of the Mioño Formation exposed in Castro Urdiales (Basque-Cantabrian Basin) are studied herein. These deposits were accumulated during a rifting phase with strong tectonic activity. The sedimentological, petrographic and cyclostratigraphic analysis demonstrates that, despite the synsedimentary tectonic instabilities and some diagenetic overprinting, the hemipelagic carbonate alternation was astronomically forced 110.68–110.47 Ma. Seasonality fluctuations driven by precession cycles caused periodic (20 ky) variations in the rate of carbonate productivity (abundance of pelagic calcareous plankton and micrite exported from adjacent shallow-water areas) and/or siliceous dilution (terrestrially derived siliciclastic sediment supply and siliceous particle production by sponges). These variations resulted in the formation of marly limestone beds when annual seasonality was low (i.e., boreal summer at aphelion, winter at perihelion) and the accumulation of marlstones when seasonality increased (i.e., boreal summer at perihelion, winter at aphelion). The incidence of these processes increased and decreased in line with seasonality modulation by short-eccentricity cycles of 100 ky. In conclusion, this study shows that Milankovitch cycles can be reliably recorded in hemipelagic successions accumulated in tectonically active settings if sediment gravity flows or other disturbances do not affect autochthonous sedimentation.