Anaerobic soil disinfestation (ASD) is a pre-plant, non-fumigant soil treatment, used to manage soil-borne pathogens, nematodes and weeds. The primary mechanism behind ASD is the manipulation of the microbiome by creating an anaerobic environment and providing labile carbon. In Florida, feed grade molasses, the carbon, and composted broiler litter are incorporated into the soil, which is then covered with a plastic mulch and watered to field capacity. ASD has been applied in both annual and perennial crops including: tomato, pepper, cucumber, strawberry, fresh cut flowers, and citrus. Plants are transplanted three-weeks post application. By combining molecular techniques and temporal sampling, shifts in the microbiome were observed during ASD treatment. Within 24 hrs. of ASD application, the microbiome shifts to an anaerobic population and the pH decreases. Throughout the treatment the microbial population is in flux. Changes in the microbiome are highly correlated to the ebb and flow of organic acids detected in ASD treated soil. ASD has an expeditious and long-term effect on the microbiome. An ASD experiment on citrus, consisted of planting three different rootstocks in ASD treated and non-treated soil. Two years post ASD application, the soil bacterial populations were significantly influenced by the non-treated rootstocks. However, rootstock had little to no influence in the ASD treated soil. While all the citrus trees tested positive for Huanglongbing, ASD treated trees had greater trunk and stem diameters, canopy, and yield compared to the non-treated trees.