Organic amendments are powerful tools for mitigating land degradation, improving soil fertility and biodiversity. Nevertheless, changes in the diversity and activity of arbuscular mycorrhizal (AM) fungi during the initial period of soil restoration under different organic amendments (e.g., crop residues and livestock manure) remains poorly understood despite their growing roles in improving soil sustainability. We conducted a six-month experiment with the application of rice straw (RS), horse manure (HM), and both amendments (RH) to an artificially degraded field in Eastern China, and the AM fungal community structure was assessed through Illumina sequencing. The dominance (35.2%) of the identified operational taxonomic units (OTUs) belonged to Glomus, whereas the majority (66.0%) of the recovered sequence reads belonged to Paraglomus. Although no notable changes in AM fungal abundance were observed, the relative abundance of Claroideoglomus significantly increased (p < .05) to 4.3% in the HM-treated soil compared with that in the control (0.1%), and Acaulospora was only detected in the three treated soils. In addition to shaping AM fungal communities, the RH appeared to be the strongest treatment for increasing AM fungal diversity, alkaline phosphatase activity, and glomalin-related soil protein (GRSP) concentrations, and these parameters were positively correlated (p < .05) with edaphic factors, notably the organic carbon concentration. Furthermore, GRSP could be used as an ecological indicator of AM fungal functioning. This study highlights that the combined application of crop residues and livestock manure could have synergistic effects that help to ameliorate the community structure and diversity of AM fungi in degraded fields.