Two-Fluid Model simulations were conducted using the commercial software Ansys CFX and Fluent to study the effect of the gas extraction on the fluid dynamic behavior of a membrane-assisted Two-Section Two-Zone Fluidized Bed Membrane Reactor (TS-TZFBMR). Simulated bubble properties and bed dynamics were analyzed and compared among different membrane reactor configurations, including reactor-wall (RWM) and immersed tubular (ITM) membranes, for their future use in catalytic reactions, e.g., alkane dehydrogenation or methane steam reforming. According to the solids hold-up distribution at different fluidization regimes and permeation fluxes, the ITM configuration is the most suitable to enhance the gas-particle contact and to favor the solids axial mixing for in-situ catalyst regeneration purposes. However, the RWM configuration provides a greater permeation area for selective gas removal and is preferred to enhance purification. It was found that relative permeation fluxes above 20% of the total feed gas have a significant impact on the fluid dynamic regime within the TS-TZFBMR, concerning the appearance of local defluidized regions, gas channeling and solids axial mixing.