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This paper presents a structural equation model to determine the job satisfaction and occupational health impacts concerning organizational and physical ergonomics, using (as a study) objective unionized workers from the University of Sonora, South Campus, as an educational enterprise, during the SARS-CoV-2 pandemic. The above is a key element of an organizational sustainability framework. In fact, there exists a knowledge gap about the relationship between diverse ergonomic factors, job satisfaction, and occupational health, in the educational institution’s context. The method used was a stratified sample of workers to which a job satisfaction–occupational health questionnaire was applied, consisting of 31 items with three-dimensional variables. As a result, the overall Cronbach’s Alpha coefficient was determined, 0.9028, which is considered adequate to guarantee reliability (i.e., very high magnitude). Therefore, after the structural equation model, only 12 items presented a strong correlation, with a good model fit of 0.036 based on the root mean square error of approximation, 1.09 degrees of freedom for the chi-square, 0.9 for the goodness of fit index, and a confidence level of 95%. Organizational and physical factors have positive impacts on job satisfaction with factor loads of 0.37 and 0.53, respectively, and p-values of 0.016 and 0.000, respectively. The constructs related to occupational health that are considered less important by the workers were also determined, which would imply a mitigation strategy. The results contribute to the body of knowledge concerning the ergonomic dimensions mentioned and support organizational sustainability improvements in educational institutions and other sectors.