This dataset contains data for soil physical and chemical properties of gypsum and non-gypsum soils in the northern Chihuahuan and eastern Mojave Deserts. Data were obtained from 20 study sites total, 10 located on soils derived from gypsum parent material and 10 located on soils derived from non-gypsum parent materials. Sites were grouped into 10 pairs, in which every gypsum site was partnered with a non-gypsum site located in the same region. Apart from soil type, partnered-site characteristics (topography, climate, elevation, slope, aspect, and presence of biocrusts) were held relatively constant. Site info and characteristics data can be accessed at knb-lter-jrn.210616001. Soil physical properties included: percent gravel, percent < 2mm fraction, soil aggregate stability, and soil compaction. Soil chemical properties were: percent gypsum content, pH, EC, and soil soluble concentrations of calcium, magnesium, potassium, sulfur, and phosphorus. The resulting soil data was used to understand physical and chemical differences between gypsum and non-gypsum soils and to examine how biocrust community types and moss species abundance and composition were associated with the measured soil variables. This study and dataset are complete.