The present research work aims to elucidate kinetics and mechanisms of the inactivation of Bacillus subtilis spores by a surface micro-discharge (SMD) - cold atmospheric pressure plasma (CAPP). Regarding industrial applications, the inactivation of spores was also studied for a static layer of a biopolymer powder or film, with an air plasma and at ambient pressure. Close to 4 log10 cycles of inactivation of Bacillus subtilis spores were achieved when exposing spores on flat glass to the SMD-CAPP. This effect can be reached at a very low plasma power density of 5 mW/cm2 in 7 min exposure time. The maximum inactivation level of spores drops when treating corn-starch powder to 2.6 log10 cycles at 7 mW/cm2 plasma power density for 5 min and with a polymer load of 5 mg/cm2. Similar is true for films produced with hydroxymethyl cellulose (HMC). The inactivation efficacy can be tuned and is a function of applied surface energy (product of the plasma power density and the exposure time) and the polymer load. Plasma diagnostics reveal the fundamental importance of reactive nitrogen species (RNS) in the inactivation. Etching of spore hull is supposed to be triggered by the plasma density, while UV-C and UV-B radiation do not contribute directly and significantly to the inactivation effect at least in a biopolymer matrix. Fluidization of a fixed powder layer is supposed to overcome limitations of the inactivation efficacy by reducing the diffusion distance of active plasma species between the source and the sample. The combination of low plasma power density with short treatment time is supposed to reduce the risk of the formation of side-products from the matrix.