The irrigated areas along the Yellow River in central Gansu Province form one of the main potato growing regions in China. However, continuous monoculture practices, which are required for intensive production in order to maximize profits, have already impaired the development of the potato industry in the region. This is reflected in severe production losses in terms of tuber yield and quality, in the poor growth and development of potato plants, and in rapidly increasing problems related to fungal soil-borne diseases. In this study, we combined the application of soil disinfection and bio-organic fertilizer amendment to recover potato plant productivity in a continuously monoculture system. Additionally, efforts were made to improve the micro-environment of the potato rhizosphere by inhibiting soil-borne pathogens via soil disinfection prior to sowing the potatoes and then directly irrigating plants with bio-organic fertilizer mixed with water injected into potato rhizosphere after potato emergence. The commercial bio-organic fertilizer used contained a large amount of plant growth-promoting rhizobacteria as well as antagonistic microorganisms active against known soil-borne fungal pathogens. Irrigation with bio-organic fertilizer was performed three times at 20 day intervals during the entire growing period of the potato plants. Field experiments were conducted in two plots that had previously displayed severe continuous monoculture-related problems, one of which had been continuously planted with potato crops for over five years and the other for over six years. The goal was to evaluate the effects of a combined application of soil disinfection and bio-organic fertilizer amendment (ABR treatment) on the management of problems related to continuous potato monoculture. The field experiment included a control (CK) and an ABR treatment with three replicates of both. Specifically, the study examined tuber yield and quality, physiological characteristics of potato plants, and the structure of the soil fungal community in a long-duration monoculture system with and without soil treatment. Compared with CK, the ABR treatment significantly increased tuber yield and the ratio of marketable tubers by 71.1% to 152.1% and 39.2% to 53.3%, respectively. No distinct differences were observed between the chemical qualities of potato tubers produced by ABR or CK treatments. In terms of the physiological characteristics of potato plants, the ABR treatment significantly increased the chlorophyll content of leaves and the root vigor as compared to CK, but decreased the MDA content both in leaves and in roots, indicating that the ABR treatment could improve growth and development of potato plants in a continuous monoculture system. Based on Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE), the ABR treatment significantly affected the structure of soil fungal community, since fungal diversity index was significantly lower in ABR than in CK. Additionally, the ABR treatment effectively suppressed soil-borne diseases, with plants exhibiting a lower incidence of disease and a lower ratio of diseased tubers from 67.2% to 82.2% and 69.1% to 70.5%, respectively, when compared with CK. Real-time PCR assessment confirmed that the abundance of several pathogenic soil fungi (Rhizoctonia solani, Fusarinm solani, and Fusarium sambucinum) in the ABR treatment was significantly lower than that in CK during the potato growth stage. In the present study, the highly significant linear correlation were revealed between tuber yield and plant disease incidence, fungal diversity index, and the abundance of soil-borne pathogens, respectively. The combined application of soil disinfection and bio-organic fertilizer amendment is a potential approach to managing problems related to continuous potato monoculture in the irrigated areas of the Yellow River floodplain in central Gansu Province since it suppresses soil-borne diseases and improves the structure of the soil microbial community.