The mass transfer of slug flow, a widely applied flow pattern in microreactors, is still difficult to predict mainly due to the competing nature between convection and diffusion. This work focused on the influence of the mixing mechanism on the mass transfer performance under gas–liquid and liquid–liquid slug flow, in both continuous slugs and dispersed droplets. Colorimetric study with the resazurin oxidation system was implemented, where the mass transfer resistance was constantly located in the aqueous phase. In the hydrophilic glass microreactor, the convection featured by intensive internal circulation and/or inter-slug leakage flow dominated diffusion, leading to nearly-constant kLa along the channel under given flow rates. However, in the hydrophobic PTFE capillary, the stagnant region constituted a significant share in the aqueous droplet, indicating the prominent role of diffusion against convection therein. As a result, kLa values decreased along the main channel length in fixed operating conditions. Accordingly, prediction models were respectively correlated depending on mixing mechanisms. Moreover, mass transfer contributions from the bubble and droplet formation stages were also investigated. This work is expected to shed light on judicious process design and reliable predictions in microreactor operations.