Although the consumption of organic produce has dramatically increased in recent years and many outbreaks continue to occur, the microbiological safety of organic produce has not been fully assessed. This study generated microbiological data to evaluate organic produce safety and also assessed the impact of growing methods (ground cover effects) and handling methods (washing practices) in organic lettuce systems. The study evaluated microbiological safety of pre- and post-harvest fresh produce samples from small organic farms in Maryland, the effect of mulching on survival of indicator bacteria and the impact of post-harvest washing method on microbiological safety and epiphytic bacterial communities. Results indicate that (1) washed post-harvest produce had higher risks than unwashed and pre-harvest organic produce as measured by indicator bacteria E. coli, total coliforms, APC, yeast and mold; (2) different mulches affected the microbial levels differently; (3) different washing methods altered the bacterial communities both immediately and following 5 days of storage. This study presents data that could be used to assess food safety risks of organic produce associated with their cultivation and on-farm handling practices.