Background: Ginger bacterial wilt is the most destructive disease that causes qualitative and quantitative rhizome yield losses in Ethiopia. Field studies were conducted to assess yield loss caused by bacterial wilt of ginger in different wilt management systems at Teppi and Jimma, Ethiopia, during 2017. Management systems were host resistance (Boziab and Local) and cultural practices (lemon grass, potassium fertilizer and soil solarization), which were applied as sole and in different levels of integrations. The experiments were factorial arranged in a randomized complete block design with three replications. Disease, growth, yield and yield-related data were collected from central rows of each experimental plot. Data were subjected to analysis of variance using linear general model (GLM) procedure of SAS version 9.3. Mean separation was made using least significant difference test. Correlation among parameters and linear regression of rhizome yield versus final wilt incidence were computed using Minitab 14 statistical package. Results: Analysis of variance indicated that variety, cultural practices and variety × cultural practice interaction effects significantly reduced wilt incidence and increased rhizome yield and its components. Variety Boziab recorded relatively more yield and yield components than the Local variety. Rhizome yield gains of about 51.4% in Local and 51.9% in Boziab at Teppi and 39.4% in Local and 49.1% in Boziab at Jimma were obtained due to integrated application of lemon grass with soil solarization and soil fertilization. The mean relative yield loss calculated for control plots due to bacterial wilt ranged from 51.4 to 51.9% at Teppi and 39.4 to 49.1% at Jimma. The lowest relative yield loss was computed from plots treated with either lemon grass with soil fertilization and solarization or lemon grass with soil fertilization. Final wilt incidence was inversely and highly significantly (P ≤ 0.001) correlated (r = − 0.90** and − 0.88**) with rhizome yield of Boziab and Local, respectively, at Teppi. The slope of the regression line also estimated that for each unit increase in percent of final mean wilt incidence, there was a rhizome yield reduction of 0.18 t ha −1 for Boziab and 0.19 t ha −1 for Local variety at Teppi. Similar trends were observed at Jimma. Moreover, the most integrated treatment provided higher net benefit with optimum marginal rate of return than others. Conclusion: The overall results indicated that integration of host resistance with cultural practices reduces yield loss, improves ginger productivity and significantly reduces bacterial wilt epidemics, and thus, it is recommended in the study areas and other related agroecologies.