The effect of addition of organic materials (shredded pruning residues, composted olive mill by-products) on spatial distribution of soil chemical and microbial properties in irrigated and rainfed olive groves was investigated. Most of the soil parcels were subjected to reduced tillage or no tillage practices. Soil sampling took place in 40 olive groves in the region of Messinia, south-western Peloponnese, Greece during a five-year period (2012–2017). The results showed significant increases in soil organic matter, humic acids and nitrate content at the end of the study period, compared to the first year of the soil sampling campaign. On the other hand, the relatively low amount of fresh organic materials that was applied to the soil produced unfavorable results. Differences between irrigated and rainfed soil parcels were not significant, for most of the soil properties, since the area receives much higher loads of rain than the average rainfall, as registered in the main olive growing regions of Greece. The area underneath the tree canopy favors an environment that enhances soil fertility, compared to the area out of the tree canopy. Changes of soil properties according to depth showed that the surface soil in olive orchards has the potential to sequester carbon and nutrients.