This dataset presents benthic foraminiferal δ¹⁸O chronostratigraphies and associated uncertainties for Ocean Drilling Program (ODP) Site 1090, based on different tuning targets including LR04 (Lisiecki and Raymo, 2005), LR09 (Lisiecki and Raymo, 2009), CENOGRID (Westerhold et al., 2020) and Probstack (Ahn et al., 2017) and based on manual versus automated tuning techniques (Middleton et al., 2024). The benthic foraminiferal δ¹⁸O record at ODP Site 1090 is based on Cibicidoides wuellerstorfi and was previously published in Hodell et al. (2000) and Venz and Hodell (2002). Automated tuning is based on Hidden Markov Model (HMM)-Match-based alignments (Middleton et al., 2024) generated using the automated probabilistic HMM-Match algorithm of Lin et al. (2014). The manual alignments of ODP Site 1090 were obtained by realigning the original age model tie points (Venz and Hodell, 2002) to the benthic foraminiferal LR04 δ¹⁸O stack using the QAnalySeries software (Kotov and Pälike, 2018). The dataset provides the basis for investigating and discussing the uncertainties of benthic foraminiferal δ¹⁸O stratigraphies for conventional manual and automated tuning techniques and evaluate their impact on sedimentary age models over the past 2.9 Myr (Middleton et al., 2024).