Hydrodynamic force loading platforms based on acoustofluidics have been developed to study the mechanical deformation of cancer cells and to control cell behavior. However, so far there have been no experimental measurements on living plant cells using such an acoustic approach. Unique structures, including cell walls, allow plant cells to exhibit more variation in mechanical resistance. In this work, we analyzed plant cell deformation and membrane permeability using a gigahertz (GHz) acoustofluidic system. By recording the proportion of intact cells in the cell population, we evaluated the mechanical resistance of the protoplasts to the hydrodynamic forces of the acoustic streaming. The results showed that a regenerated primary cell wall (PCW) could significantly improve the mechanical resistance of individual plant cells within 24 h compared to the freshly prepared protoplasts without walls. The results of enzymatic degradation showed that three main components of the primary cell wall contribute to different degrees to the improvement of the mechanical properties of the cells, in decreasing order: cellulose, hemicellulose, and pectin. Furthermore, we have shown that such an acoustofluidic system can alter the permeability of the protoplast membrane in a controllable manner for transient gene expression.