Soil moisture is a key link between hydrologic and ecologic processes in desert shrublands. Understanding how soil moisture is spatially distributed in desert shrublands provides valuable insights into how shrubs use and impact limiting water resources, and how shrublands may respond to future meteorological and climate change. Our goals were to determine how soil moisture is partitioned between soil volumes under canopies and in the bare soil interspaces across multiple desert shrublands, and to evaluate the roles of physical soil properties, shrub-type characteristics, meteorology, and measurement resolution in influencing and observing variation in soil moisture partitioning. Utilizing two long-term soil moisture datasets (monthly resolution, 30 years, whole soil profile measurements; and 30 min resolution, 10 years, 10–30 cm measurements), we compared soil moisture partitioning across nine northern Chihuahuan Desert shrubland sites (three sites dominated by creosotebush [Larrea tridentata], three by honey mesquite [Prosopis glandulosa], and three by tarbush [Flourensia cernua]) in the Jornada Basin, southern New Mexico, USA. Over 30 years, monthly, whole profile data showed that soil moisture in mesquite shrublands was consistently higher in bare soil interspaces compared to under canopies, whereas soil moisture under and between shrubs was more similar in creosotebush and tarbush shrublands. Physical soil properties were linked as explanatory variables of long-term soil moisture partitioning (monthly whole profile dataset), whereas 30-minute data showed that shorter-term periods of higher precipitation promoted greater near surface soil moisture (10–30 cm) in bare soil interspaces that was not captured at monthly time steps. Thus, although the long-term average partitioning of soil moisture in these shrublands is strongly controlled by soil physical properties, soil moisture partitioning varies at shorter timescales (daily to weekly) in response to precipitation events. Moreover, shrub-type characteristics influenced soil moisture partitioning, with dense and tall mesquite shrubs having lower under canopy soil moisture than tarbush, and root architecture potentially influencing partitioning across creosotebush sites. These results illustrate diversity in soil moisture partitioning both between and within shrublands of the northern Chihuahuan Desert, and elucidate how physical soil properties, shrub-type characteristics, and meteorological variation interact to shape their soil moisture dynamics.