Background and aims It has been confirmed that the declines in arbuscular mycorrhizal fungi (AMF) populations and agroecosystem diversity are largely due to nutrient enrichment caused by fertilization. Replacing chemical-only fertilization with organic fertilization is widely considered a possible approach for maintaining soil biodiversity and a healthy functioning ecosystem. Here we aim to examine the effects of organic fertilizer on AMF occurrence. Methods We conducted a meta-analysis of 162 field experiments from 54 published studies conducted over the last 20 years. Our dataset included two groups: organic fertilization (OF) vs chemical-only fertilization (CF) and OF vs no fertilization (NF). Results We found that organic fertilizer increased AM fungal biomass and was less detrimental to AMF richness than mineral-only fertilization. AMF responses to organic fertilizer were generally positive when AMF and host plants had a strong mutualistic symbiosis such as in phosphorus-deficient soil, drought and semi-drought areas, at low latitudes, and at testing sites that contained two or more plant species or included legume. In conditions other than these, the responses were generally negative. Organic carbon input, increased soil phosphorus and the ratio of fertilizer N and P jointly explain the effects of organic fertilizer on AMF occurrence. Conclusions Our analysis indicates that, although some limiting factors exist, application of organic fertilizer can be an effective practice to protect AM symbiosis from the negative effects of nutrient enrichment in current cropping systems.