The San Joaquin Valley produces more than 250 unique crops and much of the U.S. fruits, vegetables, and nuts. One of the main limiting factors for production in this region is reduced availability of water. Deficit irrigation is a management practice where plants receive less than full irrigation but only at certain growth stages to minimize yield loss or long-term impacts to the crop. Given the multiple roles of soil microorganisms in the soil system, it is important to asses any impact of deficit irrigation on soil microbial communities. In the present study, full and deficit irrigation treatments were applied for 7 years using furrow, microsprinkler, and surface drip irrigation systems in a peach orchard. In the seventh year, soil samples were collected before and after implementation of deficit irrigation treatments to investigate effects on soil microbial community biomass and composition. Results showed that the proportion of Gram-positive bacteria and actinomycetes were significantly higher in furrow irrigation, whereas fungi and Gram-negative bacteria were lower in proportion under furrow irrigation as compared with microsprinkler and drip irrigation methods. Canonical variate analysis showed that soil microbial communities markedly differed after deficit treatment in furrow and microspray irrigation, but remained similar in surface drip irrigation in deficit and full irrigation. This may be due to frequent irrigation in surface drip where soil surface remained moist most of the time as compared with furrow and microsprinkler irrigation methods where irrigation was less frequent.