Olive mill wastewater (OMW) is the main residual product of olive processing and its disposal can represent a relevant environmental issue in Mediterranean countries, where olive oil production is large and concentrated in a short-lasting period. OMW is characterised by high pollutant load, salinity and phytotoxic levels of polyphenols, but also by a high amount of organic compounds and plant mineral nutrients. Therefore, OMW field spreading may represent a low cost contribution to crop fertilisation and soil amendment. Here, we assessed the short- and long-term effects of long-lasting repeated OMW applications on soil chemical and biochemical properties and arbuscular mycorrhizal fungi (AMF). In addition the influence of two OMW management strategies, characterised by different seasonality of spreading (autumn and spring times) was evaluated. Soil was amended by 0 and 80 m3 ha−1 of OMW. Principal coordinate analyses (PCO) together with PERMANOVAs showed that long-lasting repeated OMW spreading: (i) affected the main soil chemical and biochemical parameters in the short-term, whereas did not determine long-term residual effects irrespective of the application times; (ii) decreased AM fungal root colonisation both after autumn and spring OMW applications; (iii) improved arbuscule occurrence in the short- and long-term for both disposal times. Therefore, at least regarding the monitored parameters, we can argue that OMW may be utilised as organic amendment in agriculture under controlled conditions given the short-term negative effects on soil quality, which can be considered negligible after a suitable waiting period.