Soil multifunctionality is closely tied to soil health, yet a comprehensive understanding of this link in agricultural soils is lacking. The aim of this study was to understand how long-term fertilization practices affect the provision of multiple services by comparing the multifunctionality of soils. The three objectives were to (i) determine whether the effect of fertilization is consistent across soil types, (ii) describe the effect of the different fertilizers on soil multifunctionality, and (iii) identify soil chemical properties that can be easily used proxies of soil multifunctionality. The descriptors belong to three functioning indexes associated with nutrient availability, carbon transformation, and soil structure maintenance. This study is the first to investigate the effect of a variety of organic fertilizers on the health of three soil types by combining physical, chemical, and biological indicators in sugarcane agroecosystems. An increase in soil multifunctionality was obtained, with no effect on yield. The effect of fertilizers was consistent across soil types. Filter mud and green waste compost significantly increased the multifunctionality and functioning indexes compared to mineral fertilizer. Modifications in soil properties did not fully explain the observed variations. Our results confirm the high potential of organic fertilization to improve multifunctionality and provide ecosystem services.