Organic agricultural systems are focused on reducing the use of chemical fertilizers and pesticides use and on improving agriculture production and soil ecosystem health. Despite the most familiar roles of soil microbial in farming systems, there is still a limited awareness and understanding of the long-term response of functional diversity in organic and conventional farming systems. In this study, we investigate the functional diversity response of the soil microbial to a) organic monoculture, b) organic polyculture; c) conventional monoculture; and d) conventional polyculture. Experiments used soil samples from the SQU agriculture station long-term greenhouse perennial fruit tree trial, which at the moment of sampling had been in place for four consecutive years. The effect of cropping systems on soil health was studied through their impact on soil microbial enumeration, resilience, functional and taxonomic diversity. The MicroRespTM assay was used to assess microbial use of different carbon sources (function) through their respiration response. This substrate-induced respiration was performed using 18 carbon substrates to determine the microbial community response to organic acids, bases, sugars, and amino acids. For this MicroRespTM assay, organic farming soils exhibited slightly lower Shannon diversity index values compared to conventional farming, suggesting a less functionally diverse microbial community in the soil. However, organic farming displayed higher values of evenness and equitability, indicating a more balanced distribution in response to different carbon sources. Furthermore, polyculture systems exhibited higher functional diversity values compared to monoculture, emphasizing the importance of crop diversity in promoting functional diversity. Soil samples were subjected in vitro to drought, heat, and heat+drought stresses. The drought treatment samples were kept in the open air for a week at 20-30 oC until around 2% (w/w) of soil moisture was reached. For the heat treatment, both dry and moist soils (15% w/w) were subjected to 50 ˚C for 3 days in a growth chamber. After the stresses were applied, soil microbial respiration was monitored for a 30-day incubation period, to assess microbial recovery. Results indicated that, organic management practices generally exhibited higher stress resistance compared to conventional farming soils, although organic amendments slightly decreased the resilience of soil microbial communities to all stresses. This decrease could be attributed to the presence of organic amendments that promote the population of less-resilient microbes. The taxonomic diversity of soil microbial communities under different abiotic stress conditions using 16S rRNA sequencing revealed distinct patterns in taxonomic diversity among various farming systems and stress conditions. Organic farming practices, both monoculture (citrus) and polyculture (citrus and mango), were found to promote higher taxonomic diversity compared to conventional farming systems under normal (non-stress) conditions. Furthermore, organic farming systems displayed greater resilience to drought and heat stresses, maintaining higher taxonomic diversity after both stresses applied individually. However, when both drought and heat stresses were combined, all farming systems experienced a substantial reduction in taxonomic diversity and the soil management effect was not evident. These findings provide valuable insights into the benefits and limitations of organic and conventional agriculture in nurturing soil health and bolstering its resilience. By recognizing soil as a living ecosystem, we can make informed decisions to promote sustainable agricultural practices that optimize the intricate dynamics of the soil microbial community, fostering long-term ecological balance and productivity.