Thin films of poly(3-hydroxybutyrate) were modified by microwave ammonia plasma treatment. The results of the modification were studied by means of contact angle goniometry, ellipsometry, Fourier transform infrared-attenuated total reflection spectroscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. To prove the presence of amino groups on the poly(3-hydroxybutyrate) surface, chemical labeling with 4-trifluoromethyl benzaldehyde was performed before X-ray photoelectron spectroscopy analysis. Under the applied plasma conditions, a hydrophilic surface with a good long-term stability was obtained.