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• Soil microbial community profiles were significantly altered in the degraded patches. • Soil microbial abundance remained unaffected by the degraded path formation. • Degraded path formation increased soil nitrifier and plant pathogen proportions. • Degraded path formation altered the soil microbial co-occurrence pattern. • Degraded path formation impeded the recovery of degraded alpine meadows. Approximately half of global grasslands are degraded. Although soil microbes play a key role in ecosystem functioning, their response to grassland degradation has not been fully investigated. In particular, degraded patch formation is the main feature of alpine meadow degradation, but little is known about its effect on soil microbes. In this study, soils were collected from three patch-degraded Tibetan alpine meadows to examine the effects of degraded patch formation on soil microbial communities. The alpine meadows at the three sites were in the third to fifth stages of degradation, respectively. Soil microbial abundance and community structure were determined through real-time PCR and MiSeq sequencing, respectively. The results showed that the degraded patch formation significantly decreased microbial respiration rates, changed the interaction patterns among microbial taxa, and increased fungal diversity, but did not significantly affect microbial abundance. Additionally, both prokaryotic and fungal community composition was significantly altered by the degraded patch formation. The functional predictions based on FAPROTAX and FUNGuild suggested that degraded patch formation significantly increased the proportion of nitrifiers, plant pathogenic fungi, and saprotrophic fungi, especially when mattic epipedons were eroded. The increased relative abundance of nitrifiers and pathogenic fungi can aggravate the risk of nitrogen leaching and plant diseases, respectively. Therefore, degraded patch formation can impede the recovery of degraded alpine meadows by changing soil microbial community composition. [ABSTRACT FROM AUTHOR]