The kinetic resolution of 3-aminopyrrolidine (3AP) and 3-aminopiperidine (3APi) with ω-transaminases was facilitated by the application of a protecting group concept. 1-N-Cbz-protected 3-aminopyrrolidine could be resolved with >99% ee at 50% conversion, the resolution of 1-N-Boc-3-aminopiperidine yielded 96% ee at 55% conversion. The reaction rate was up to 50-fold higher by using protected substrates. Most importantly, enantioselectivity increased remarkably after carbamate protection compared to the unprotected substrates (86 vs. 99% ee). Surprisingly, benzyl protection of 3AP had no influence on enantioselectivity. A possible explanation for this observation could be the different flexibility of the benzyl- or carbamate-protected 3AP as confirmed by NMR spectroscopy.