Due to its high chemical specificity, nondestructive nature and sub-micron resolution, O-PTIR imaging has found widespread application in both nanoparticle and life science research. In a transmission configuration, the technique is capable of optical sectioning and can even be used for measurement in aqueous environments, e.g., within the channels of a microfluidic chip. However, accommodating a microfluidic chip in a confocal microscope system necessitates certain design changes, which come at the expense of spatial resolution and the size of the instrument. Furthermore, although similar to optical imaging in the radial plane, the photothermal signal has a two-lobed shape in axial direction, making photothermal z scans inherently prone to artifacts. We will explain specific design choices for O-PTIR imaging in microfluidic channels and present theoretical and experimental data to investigate the spectral fidelity and optical sectioning capabilities of O-PTIR transmission systems.