Early fluid mixing in channel flows without incurring much drop in the pressure head is desired in industrial applications. This study explores wall-mounted flexible plates as obstacles to enhance mixing in channel flows. Using fluid–structure-scalar interaction simulations, we investigate the oscillations of the flexible plates under the flow, which serve as a vortex generator and help increase the mixing. The channel flow involves a scalar field with distinct concentrations initially separated across the channel, gradually intermixing due to vortical structures of varying scales. We have used the “mixing index” and “head loss” metrics along the channel length to assess the mixing quality when plates with different flexibility (characterized by the Cauchy number, Ca) are used. This study introduces a comprehensive criterion, the “coefficient of performance,” derived by comparing mixing and head loss in the presence and absence of obstacles. Aggregating results across various Ca values reveal that flexible plates substantially improve fluid mixing compared to rigid plates. We have also investigated the effect of the pulsatile fluid inlet (quantified by Strouhal number, Stf) and found that lower inlet flow pulsation (Stf<32) adversely impacts mixing performance, recommending a steady inlet flow. However, at high Stf, specifically in the configuration with Ca = 0.06 and Stf = 32, the best mixing performance is achieved in the channel, which marginally outperforms the steady inlet case. The conclusive takeaways from this study are that the plates with increased flexibility result in better mixing, and high inlet pulsation can be employed to fine-tune the mixing performance for further enhancement.