The middle Miocene Valdearenas–Muduex section in the internally-drained, continental Madrid Basin (central Spain) is dated bio-magnetostratigraphically between 15.2 Ma and 11.5 Ma. The section contains two formation-scale, sedimentary sequences, that both consist of a siliciclastic lower part and a calcareous upper part. Siliciclastic sedimentation took place in distal floodplain and fluvial environments, while limestones resulted from carbonate precipitation in calcic soil profiles and in ephemeral lacustrine water bodies. Spectral analysis of the L* colour time series points to the influence of the ∼ 405-kyr and 0.97-Myr eccentricity cycles, while the bases of the two calcareous intervals correlate to successive minima of the 2.4-Myr eccentricity cycle. The 405-kyr cycle lags maximum eccentricity, whereas the 0.97 and 2.4-Myr cycles lag minimum eccentricity, each by approximately a quarter of a cycle. No obliquity forcing is detected. The observed orbital configuration of 2.4-Myr minima at the base of limestone-dominated intervals is similar to a previously documented Late Miocene shift in the Teruel Basin of northeast Spain. Our results indicate that long-period eccentricity climate forcing may well be a significant player on long, tectonic time scales in continental basin fill.