This dataset merges nitrogen data from the Yedoma domain. It includes numerous fieldwork campaigns, which take place since 1998. In total 467 samples from the active layer (seasonally thawed layer), 175 samples from perennially frozen Holocene cover deposits, 479 samples from thermokarst deposits in drained thermokarst, 175 in-situ thawed, diagenetically (anaerobic microbial decomposition possible during unfrozen phase) altered Yedoma deposits (called Taberite), and 917 samples from frozen Yedoma deposits are included. Moreover it includes a NH4+ and NO3- quantification basing on of 658 samples, including 378 data points for NH4+ (active layer, 93; Holocene cover, 108; thermokarst sediment, 138; Taberite, 0; Yedoma deposit, 39) and 542 data points for NO3- (active layer, 94; Holocene cover, 137; thermokarst sediment, 119; Taberite, 6; Yedoma deposit, 186). The bootstrapping code we adjusted for this study is available from Zenodo (Jongejans & Strauss, 2020, doi:10.5281/zenodo.3734247). The code is published under a GNU General Public License v3.0. The included areal estimation of the Yedoma domain was used from the IRYP database (Strauss et al., 2022, doi:10.1594/PANGAEA.940078).