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In semi-arid Mediterranean environments, the loss of soil fertility can be avoided through the optimization and innovation of low environmental impact agricultural techniques. Such 'innovative', suitable agricultural management practices can have positive effects on soil microbial communities. The aim of the present study was to explore the effects of two different agricultural systems ('innovative' and 'conventional') on the diversity of important groups of microorganisms related to soil fertility, such as fungi, actinomycetes, Pseudomonas spp., Bacillus spp., Azotobacter spp., proteolytic and ammonifying bacteria. The study was carried out in an apricot orchard located in Southern Italy. Since 2003, half of the orchard was managed adopting no-tillage, cover crops, compost application, drip irrigation, winter pruning and limited mineral fertilization, whereas the other half was subjected to 'conventional' management. Soil samples were randomly collected from the superficial soil layer in four different orchard positions: innovative along the inter-rows (IIR) and under drip emitters (IUE), and conventional along the inter-rows (CIR) and under drip emitters (CUE). Higher populations of total bacteria, actinomycetes and proteolytic bacteria were induced by IIR treatment, whereas Pseudomonas spp., Azotobacter spp. and ammonifying bacteria showed increased populations in IUE. No differences between the treatments were found for total fungi and Bacillus spp. The higher inputs of organic matter of innovative plots caused an increase in the microbial groups responsible for nitrogen metabolism in well-watered zones (IUE), and higher activities of decomposer and humus-forming microorganisms in IIR. Results show that suitable agricultural practices can have positive effects on microbial activities and complexity, which in turn influence soil fertility.