Maintaining and enhancing soil biological processes is essential for ecosystem health. However, the effects of different farming practices on soil microbiomes remains underexplored. We aim to assess how varying levels of crop diversity and intensity influence microbial populations and their beneficial functions. Seven farming systems (FS) treatments from a long-term field trial in Queensland were selected to represent different levels of cropping diversity and intensity. A multi-omics approach, including amplicon metagenome sequencing and biochemical assays, was employed to evaluate practices promoting diverse microbiomes and stable biological functions. Cropping intensity was found to be a primary driver of bacterial diversity across systems, irrespective of crop diversity. In the pasture system, low crop diversity significantly affected bacterial diversity despite high cropping intensity. Fungal diversity showed varied responses depending on the alpha diversity metrics used, indicating a community structure characterized by high OTU richness but low evenness in the higher intensity system. Positive correlations were observed between microbial abundances and system intensity levels. Over six years of treatment, the increase in bacterial community diversity plateaued, with the highest diversity in treatments with high crop diversity. Conversely, arbuscular mycorrhizal fungi were significantly more abundant after nine years of treatment compared to the start of the trial, with the greatest increase in the higher intensity system. Network analysis confirmed a strong correlation between community complexity/ connectivity and intensity levels. The abundance of 12 functional genes involved in C and nutrient cycles, as well as microbial catabolic diversity responses, showed similar trends. This functional microbial ecology approach applied in a FS setting provides an integrated view of responses in microbial functionality. The findings suggest that increasing cropping intensity, more than crop diversity, enhances soil microbial diversity and functions, which could guide the development of farming systems and soil health management.