Preserving minimally processed fruits represents a technological challenge. Therefore, non-thermal plasma (NTP) is proposed as one of the preservation methods. The aim of this work was to evaluate the effect of the application of NTP before and after packaging sliced apples in two films: One with high and another with low oxygen barrier features. Different parameters were evaluated during 14 days at 4 °C. Samples treated before packaging showed lower crunchiness and browning development, as indicated by chromatic and textural parameters. NTP reduced mesophiles, psychrotrophs, and yeasts and molds on the slices by 1–2 log units, although it had no effect on the antioxidant content of the apple slices, which were better preserved with high-barrier packaging. Samples treated with NTP, and low barrier packaging showed lower sugar content on day one. When applied after packaging, NTP contributed to better preservation of slice microstructure and tissue viability. Results showed that the combination of NTP applied after packaging and high-barrier film was the most suitable for maintaining fruit quality, mainly by better preserving slice color. In turn, tissue microstructure, texture analysis, and viability tests also supported this conclusion.