Long-term field experiments provide key insights into whether organic amendments can enhance soil health and the sustainability of Mediterranean perennial cropping systems. However, their persistent effects on soil microbial communities and crop quality remain insufficiently understood, especially under semiarid Mediterranean conditions. This research assessed the long-term effects of repeated compost and biochar applications on soil organic matter, microbial communities, and the nutritional and phytochemical status of a mature olive orchard (Olea europaea L. cv. Arbequina). Four treatments based on biennial organic amendments over a decade were evaluated: (i) control, (ii) compost, (iii) compost-biochar mixture (90:10, dry weight), and (iv) biochar. Soil microbiome analysis via high-throughput sequencing of the 16S rRNA and ITS regions revealed no lasting alterations after four applications over ten years compared with the control without amendment. However, high-resolution seasonal sampling after the fifth amendment indicated distinct, primarily fungal, community shifts. Yet recovery to the original state highlights the resilience of these microbial communities to anthropogenic inputs. In contrast, fruit quality and phytochemicals in olives were more sensitive to soil management practices, with organic amendments notably influencing oleuropein concentrations in olive fruits (up to 24% lower than the control; p < 0.05, eta(2) = 0.79), while yields remained stable across treatments. This decade-long study reveals that established Mediterranean olive orchards possess a highly resilient soil microbiome that resists permanent shifts despite repeated organic amendments. However, the sensitivity of secondary metabolites-specifically oleuropein-to these practices suggests that adding phytochemical indicators provides a high-sensitivity metric for monitoring "soil health" in semi-arid perennial cropping systems. By simultaneously assessing soil, microbial, and phytochemical data over 11 years, this research provides a unique, system-level reference that captures management impacts often missed by traditional soil or yield metrics.