While acoustic-based separation has been shown before , these processes were based on the effect of acoustic forces on larger cells and the absence of an effect on the smaller bacterial cells. By contrast, in this work, we use acoustic forces to trap small bacterial cells themselves and thus enable, for the first time, semi-continuous medium exchange. Furthermore, we analyze our approach's underlying mechanisms using finite element simulations to enable the direct optimization of our design. We find that particles can only be trapped efficiently with a wall thickness below 20 µm. The fabrication of such small structures within a channel of 190 µm depth has only been achieved by wet etching, which is limited in design by the crystal orientation. For manufacturing using a much less restrictive method, we optimize our deep reactive ion etching (DRIE) process, which enables us to produce devices with a wall as thin as 13 µm in 190 µm deep channels. At a flow rate of 10 µL min -1 we are able to trap ∼ 70% of the bacteria. In a subsequent electroporation step in a benchtop electroporator, 1% of the initial bacteria are successfully transformed with an antibiotic resistance harboring plasmid. Our new design shows significant potential for future applications of BAW devices in a variety of research fields.