Soil microbial communities are crucial for ecological processes such as organic matter turnover and nitrogen cycling in agricultural soils. Studies on the soil microbiome in agricultural systems often neglect deeper soil layers and focus instead on top soils. As part of the Green Dairy LOEWE project we performed detailed studies on the soil microbiome in depth gradients from top soil layers down to one meter depth. In spring 2022, soil samples from 0-10, 10-30, 30-50 and 50-100 cm depth from one grassland and two arable plots were analyzed comparatively. On arable plot contained alfalfa at the beginning of the second year of cultivation and one had spelt and field beans as the previous crop. We determined the total abundance of Bacteria, Archaea and fungi and specific microbial groups involved in the nitrogen cycle using quantitative PCR (qPCR) assays. We further on studied bacterial and archaeal community profiles with respect to community diversity and composition in different soil layers by 16S rRNA gene amplicon Illumine sequencing. Initial data showed that microbial abundance (Bacteria, Archaea, fungi and N cycling genes) significantly decrease with soil depth with clear differences among arable and grassland soil gradients. We expect that microbial community patterns will also show clear differences within the depth gradients with system specific differences. This study gives important information of the soil microbial communities in different soil layers of grassland and arable agricultural systems and helps to select individual soil layers for specific research questions.