Background Estimation of prevalence of feeding practices during diarrhea using conventional imputation methods may be biased as these methods apply to observed factors and in this study, feeding practice status was unobserved for those without diarrhea. The study aimed at re-estimating the prevalence of feeding practices using the bivariate sample selection model. Methods The study used 2015–2016 Malawi demographic health survey (MDHS) data which had 16,246 children records who had diarrhea or not. A bivariate Joe copula regression model with 90 degrees rotation was fitted to either drinking or eating more, with diarrhea as a sample selection outcome in the bivariate models. The prevalence of drinking more than usual and prevalence of eating more than usual were then estimated based on the fitted bivariate model. These prevalences were then compared to the prevalences estimated using the conventional imputation method. Results There was a substantial increase in the re-estimated national prevalence of drinking more fluids (40.0%, 95% CI [31.7–50.5]) or prevalence of eating more food (20.46%, 95% CI [9.87–38.55]) using the bivariate model as compared to the prevalences estimated by the conventional imputation method, that is, (28.9%, 95% CI [27.0–30.7]) and (13.1%, 95% CI [12.0–15.0]) respectively. The maps of the regional prevalences showed similar results where the prevalences estimated by the bivariate model were relatively higher than those estimated by the standard imputation method. The presence of diarrhea was somehow weakly negatively correlated with either drinking more fluids or eating more food. Conclusion The estimation of prevalence of drinking more fluids or eating more food during diarrhea should use bivariate modelling to model sample selection variable so as to minimize bias. The observed negative correlation between diarrhea presence and feeding practices implies that mothers should be encouraged to let their children drink more fluids or eat more food during diarrhea episode to avoid dehydration and malnutrition.