In this study, applicability of peristaltic waves as an efficient means for bio-particle manipulation is numerically investigated using the lattice Boltzmann method (LBM). The analysis is carried out in a flow configuration which comprises a two-dimensional, closed-ended, vertical cavity filled with a Bingham fluid and equipped with two flexible side walls and two rigid upper and lower plates. It is shown that by judicially adjusting the working parameters of the peristaltic waves (e.g., wavelength, amplitude, speed, and/or phase lag) it is possible to control the dynamics/trajectory of a large, circular bio-particle immersed in the fluid. It is also shown that a suspending circular particle moves faster if the surrounding fluid possess a yield-stress. Based on our obtained numerical results, for a given cross-sectional area, circular particles move faster than elliptical particles when excited peristaltically.