Abstract Intensive cultivation in greenhouses of China has degraded the soil through acidification, salinization, and has caused an increase in soil-borne pathogens accumulation that negatively impacts vegetable production. In this study, six treatments, i.e. CK, degraded soil collected from greenhouse was irrigated to maximum field capacity and covered with plastic film; Al-RSD-F, flooding soil incorporated with alfalfa; Al-RSD, soil was incorporated with alfalfa, irrigated to maximum field capacity and covered with plastic film; Al-RSD + T37, inoculating Trichoderma harzianium T37 into soil at the end of the Al-RSD; Et-RSD, soil was incorporated with ethanol, irrigated to maximum field capacity and covered with plastic film; AW, soil was incorporated with ammonia and covered with plastic film, were conducted to investigate their effects on the physicochemical properties of degraded soil and disinfestations of Rhizoctonia solani , to control the damping-off disease in the two consecutive plantings of cucumber seedlings after the treatments. Treatments with Al-RSD-F, Al-RSD, Al-RSD + T37 and Et-RSD increased the pH and reduced the electrical conductivity of the soils, reduced population of R. solani and damping off of cucumber seedlings. These treatments with exception of Et-RSD, increased the populations of bacteria and fungi and showed higher diversity of bacteria after the second season of cucumber seedlings. Treatment AW was toxic and did not allow the survival of the cucumber seedlings. The treatments Al-RSD + T37 and Et-RSD showed the higher control of damping off, probably because the antagonist was favored by the previous treatment and could efficiently colonize the cucumber seedlings roots, and the Et-RSD was favored by the highest accumulation of toxic acetic acid in the soil. Alfalfa-amended soil disinfestations with or without Trichoderma , as well as an ethanol soil disinfestation could be used to recover degraded greenhouse soils.