Soil health is an old concept receiving renewed attention. Defined as a soil’s capacity to function, soil health is composed of physical, chemical, and biological attributes. The improvement and maintenance of soil health is considered a cornerstone of organic agriculture. Although there are numerous studies that compare organic systems with conventional systems, fewer studies compare organic systems with each other to determine how best to improve soil health metrics. In this review, we focused on nine indicators of soil health (aggregate stability, water holding capacity, infiltration/porosity, erosion/runoff, nutrient cycling, organic carbon, microbial biomass, macrofauna abundance, and weed seed bank). We found 153 peer-reviewed, published studies that measured these soil health indicators in two or more organic treatments. Overall, published research focused on four key practices: (1) cover crops, (2) organic amendments, (3) rotation diversity and length, and (4) tillage. Of these, 26 studies focused on cover crops, 77 on organic amendments, 32 on crop rotations, 40 on tillage, and 22 included more than one practice. Eighty percent of the studies were conducted in the USA and Europe. We found strong agreement in the literature that roll-killed cover crops suppressed weeds better than disking and that weed suppression required high levels of cover crop biomass. Combinations of organic amendments such as composts, manures, and vermicomposts improved soil health metrics compared to when applied alone. Including a perennial crop, like alfalfa, consistently improved soil carbon (C), nitrogen (N), and aggregate stability. Soil health metrics were improved under shallow, non-inversion tillage strategies compared with conventional tillage. Despite their importance for climate change mitigation and adaptation, the effect of practices on aggregate stability and water dynamics were under-studied compared with other soil health metrics. There is a great deal of variety and nuance to organic systems, and future research should focus on how to optimize practices within organic systems to improve and maintain soil health.