The coupled CFD-E-model for multiphase micro-mixing was developed, and used to predict the micro-mixing effects on the parallel competing chemical reactions in semi-batch gas–liquid and solid–liquid stirred tanks. Based on the multiphase macro-flow field, the key parameters of the micro-mixing E-model were obtained with solving the Reynolds-averaged transport equations of mixture fraction and its variance at low computational costs. Compared with experimental data, the multiphase numerical method shows the satisfactory predicting ability. For the gas–liquid system, the segregated reaction zone is mainly near the feed point, and shrinks to the exit of feed-pipe when the feed position is closer to the impeller. Besides, surface feed requires more time to completely exhaust the added H + solution than that of impeller region feed at the same operating condition. For the solid–liquid system, when the solid suspension cloud is formed at high solid holdups, the flow velocity in the clear liquid layer above the cloud is notably reduced and the reactions proceed slowly in this almost stagnant zone. Therefore, the segregation index in this case is larger than that in the dilute solid–liquid system. The coupled CFD-E-model for multiphase micro-mixing is developed based on the Eulerian–Eulerian multiphase flow. The micro-mixing effects on the parallel competing chemical reactions occurring in solid–liquid and gas–liquid stirred tanks are investigated using the coupled CFD-E-model with better model parameters in terms of the concept of the mixture fraction and its variance. The predicted segregation index under different operation conditions is in reasonable agreement with the experimental data.