Boron nitride (BN) is a promising 2D material as well as a potential wide‐bandgap semiconductor. Chemical vapor deposition (CVD) is commonly used to deposit single layers or thin films of BN, but the deposition process is insufficiently understood at an atomic scale. the CVD of BN is studied using two boron precursors, the organoboranes, triethylborane, and trimethylborane. Using high resolution (scanning) transmission electron microscopy and electron energy loss spectroscopy, this study shows that hexagonal‐BN (h‐BN) nucleates and grows epitaxially for ≈4 nm before it either polytype transforms to rhombohedral‐BN (r‐BN), turns to less ordered turbostratic‐BN or is terminated by a layer of amorphous carbon. this study proposes that the carbon in the organoboranes deposits on the epitaxially growing h‐BN surface and this either leads to the polytype transition to r‐BN, the transition to less ordered BN growth, or complete surface poisoning with carbon terminating BN growth. These results question the use of organoboranes in CVD of epitaxial BN films, and the polytype stability of h‐BN growing on graphene.