Soil is a natural capital which supplies valuable ecosystem services including carbon and nitrogen storage. Agroecosystems play an important role in soil organic carbon (SOC) and soil total nitrogen (NT) accumulation. The aim of this study was to analyse SOC stock (SOCS) and NT stock (NTS) in relation to land use (arable land-AL, permanent grasslands-PG), management, soil depth, and selected soil properties of six soil subtypes (Rendzic Leptosol—LPrz, Dystric Cambisol—CMdy, Stagnic Cambisol—CMst, Haplic Fluvisol—FLha, Gleyic Fluvisol—FLgl, Haplic Chernozem—CHha) which are the most widespread in Slovakia. SOCS for a 50 cm deep soil profile ranged from 161 t.ha−1 in CHha to 59 t.ha−1 in FLgl in grasslands, and in arable lands from 111 t.ha−1 in CHha to 38 t.ha−1 in CMst. In grasslands, FLs and CMst showed the significantly lowest SOCS and NTS in comparison to CMdy, LPrz, and CHha. The mean soil NT content in arable land and grasslands was 2.21 g.kg−1 and 2.82 g.kg−1, respectively. ANOVA showed that soil subtype, land use, and site have significantly affected SOCS but not NTS. The correlation analysis revealed correlations between SOCS and NTS. SOCS was also correlated with C:N, pH, P, and K. This study should help to encourage practices to maintain soil C and soil properties and to ensure the sustainability of the functions of many soil types in Slovakia.