Current industry needs are related to higher awareness of modern consumers. These consumers are looking for products in which properties such as bioactive compounds are preserved as much as possible. Plasma treatment is one of the most promising nonthermal technologies that can decontaminate food and keep its original properties. Therefore, the aim of this work was to examine the usefulness of atmospheric pressure argon microwave plasma on decontamination of black pepper seeds, allspice berries and juniper berries. The samples were irradiated by plasma for 15–60 s and their physicochemical (dry matter content, water activity, color, total phenolic content, antioxidant activity, piperine content in black pepper seeds) and microbial (bacteria and molds count) quality was evaluated afterwards. Results demonstrated that plasma irradiation for 15 s was sufficient for partial inactivation of A. niger but less effective against the Gram-positive bacterium B. subtilis, regardless of the raw material. At the same time, plasma treatment reduced water activity, which can positively affect further storage of spices. Properly selected plasma parameters may also enhance extractability of phenolics or piperine (from black pepper seeds) and improve antioxidant activity with not very great, but visible, color changes.