Sub-Milankovitch rhythmic features in sedimentary records have been reported from throughout geological time. However, their origin remains enigmatic, in particular during so-called greenhouse periods in Earth’s history. To better understand such short-term climatic changes, we sampled two 3-m-thick intervals of early Devonian hemipelagic carbonate at 1 cm resolution in the Pod Barrandovem section (Czech Republic). Greenhouse conditions prevailed during early Devonian times, and the chosen resolution enables the detection of millennial-scale climate change as recorded by elemental abundances. We used a previously published astrochronology for the section to transform the studied series from the stratigraphic into the time domain. Spectral analysis of the time-calibrated log-transformed Ti records reveal obliquity and precession cycles, confirming the applied astrochronology. Additional spectral peaks with periods of 2.3–2.7, 6–8, and 10–12 k.y. appear in both records. Furthermore, a 1.5 k.y. periodicity, close to the Pleistocene Dansgaard-Oeschger oscillation, is also identified, but only in the record with higher accumulation rate (∼3.5 cm/k.y.). Bi-coherence spectra reveal that the 6–8 and 10–12 k.y. periodic components are combination tones of Milankovitch cycles. We infer the shorter ∼2.5 k.y. periodicity to be the result of solar forcing, related to the Hallstatt cycle. These new observations strengthen the case for an external origin of millennial-scale features.