The Mid-Pleistocene Transition (MPT; 1.25–0.6 million years ago, Ma) is one of the most important and still debated climate reorganizations during which the glacial/interglacial cycles switched from a 41-thousand years (kyr) cycle (i.e. obliquity) to a quasi-periodic 100-kyr cycle (associated with orbital eccentricity). Variations in the orbital geometry can affect the abundance and distribution of certain marine biota such as the coccolithophores, a group of unicellular calcifying phytoplankton, whose skeletal remains – called nannofossils – represent a valid tool within the geological archives to infer change in surface water conditions and/or coccolithophore productivity and how orbital variations may have impacted them. Here, we apply for the first time various time series analytical techniques to the nannofossil dataset from mid-latitudinal Ocean Drilling Program (ODP) Site 1209 in the northwest Pacific Ocean for the interval spanning the last 1.6 Myr. To better interpret the orbital signal recorded by different nannofossil species we used time series analyses (i.e. wavelet, autocorrelation and cross correlation) to identify the main periodicities by single nannofossil species during the MPT, and to investigate further their response timings to those orbital drivers. In addition, we investigated how the recorded periodicities can improve understanding of the paleoecological preferences of particular species. The combination of multiple time series analyses allowed identification of the 100-kyr periodicity as the main cyclicity recorded in most analyzed species at Site 1209, documenting the predominance of the eccentricity-related signal at mid-latitudes and a reduced or absent influence of the obliquity response. Thus, our data highlight how orbital influence varies by latitude impacting the nannofossil species. The lag between eccentricity and species abundance fluctuations was also investigated, identifying a fast response ranging between 20 and 40 kyr for the taxa Calcidiscus leptoporus subspecies leptoporus, Gephyrocapsa caribbeanica small, and Reticulofenestra spp. (>5 μm). This study corroborates the potential of nannofossils to deepen understanding of the dynamics and effects of variations in orbital geometry through time. It also underlines the need to extend the study of the responses of specific species through the use of different time series analysis techniques in order to return complementary information and detect clearer orbital signals.