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Objectives In this paper, the effect of the position of the inlet and outlet microchannels on the flow profile and the geometry of the recognition chamber for sample pre-treatment in an electrochemical biosensor to be used in osteoporosis management were investigated. Methods All numerical computation presented in this work were performed using COMSOL Multiphysics and Fluent. Simulation was performed for a three-dimensional, incompressible Navier-Stokes flow and so explicit biphasic volume of fluid (VOF) equations were used. Results In the designed microfluidic system, a pressure-driven laminar flow with no-slip boundary condition was responsible for fluid actuation through microchannels in a reproducible approach. Based on the simulation results, the number of outlets was increased and the angel through which the inlets and outlets were attached to the microchamber was changed so that the dead volume would be eliminated and the fluid flow trajectory, the velocity field and pressure were evenly distributed across the chamber. The Re number in the inlets was equal to 4.41, suggesting a laminar flow at this site. Conclusion The simulation results along with the fact that the design change was tested using laser ablated tape and a color dye at different steps provided the researchers with the opportunity to study the changes in a fast and accurate but cheap method. The absence of backflow helps with the cross-talk concern in the channels and the lack of bubbles and complete coverage of the chamber helps with a better surface modification and thus better sensing performance.