In contrast with a thermal plasma surgical instrument based on coagulative and ablative properties, low-temperature (non-thermal) non-equilibrium plasmas are known for novel medicinal effects on exposed tissue while minimizing undesirable tissue damage. In this study we demonstrated that arrays of non-thermal microplasma jet devices fabricated from a transparent polymer can efficiently inactivate fungi (Candida albicans) as well as bacteria (Escherichia coli), both in vitro and in vivo, and that this leads to a significant wound-healing effect. Microplasma jet arrays offer several advantages over conventional single-jet devices, including superior packing density, inherent scalability for larger treatment areas, unprecedented material flexibility in a plasma jet device, and the selective generation of medically relevant reactive species at higher plasma densities. The therapeutic effects of our multi-jet device were verified on second-degree burns in animal rat models. Reduction of the wound area and the histology of the wound after treatment have been investigated, and expression of interleukin (IL)-1α, -6 and -10 was verified to evaluate the healing effects. The consistent effectiveness of non-thermal plasma treatment has been observed especially in decreasing wound size and promoting re-epithelialization through collagen arrangement and the regulation of expression of inflammatory genes.