Purpose <p>Continuous cropping (CC) of ginger often leads to continuous cropping obstacles (CCOs) and soil degradation. However, the role of allelopathy and its underlying mechanisms in this process remain unclear. This study aimed to identify allelochemicals associated with ginger CC and to explore their relationships with soil properties, microbial communities, disease incidence, and crop performance.</p> Methods <p>Analysis of rhizosphere soils from ginger fields with 0–7&#xa0;years of CC involved the identification of allelochemicals from methanol extracts, with their allelopathic effects assessed on Arabidopsis, lettuce, and ginger seedlings. Agronomic performance, microbial community structure (determined by high-throughput sequencing), soil physicochemical properties, enzyme activities, and ginger quality were measured. Relationships among these factors were evaluated using correlation analysis and partial least squares path modeling.</p> Results <p>Ten secondary metabolites of ginger were isolated and characterized as allelochemically active compounds, including five with autotoxic activity. The effects of ginger CC on the soil environmental properties, disease incidence, crop yield and quality were closely related to the increased content of the autotoxic compounds. It is hypothesized that these compounds regulate plant growth and influence rhizosphere microbial community structure, soil enzyme activities and nutrient uptake. They showed significant positive correlations with pathogenic fungi and negative correlations with beneficial bacteria.</p> Conclusions <p>These results support the hypothesis that autotoxic allelochemicals and rhizosphere microbial communities in ginger CC disrupt soil ecological balance, leading to growth inhibition and reduced productivity. Reducing these compounds may offer an effective strategy to restore soil health and sustain ginger cultivation.</p> Graphic Abstract <p></p>