There is growing interest among the public and scientific community toward the use of probiotics to potentially restore the composition of the gut microbiome. With the aim of preparing eco-friendly probiotic edible films, we explored the addition of probiotics to the seed mucilage films of quince, flax, and basil. These mucilages are natural and compatible blends of different polysaccharides that have demonstrated medical benefits. All three seed mucilage films exhibited high moisture retention regardless of the presence of probiotics, which is needed to help preserve the moisture/freshness of food. Films from flax and quince mucilage were found to be more thermally stable and mechanically robust with higher elastic moduli and elongation at break than basil mucilage films. These films effectively protected fruits against UV light, maintaining the probiotics viability and inactivation rate during storage. Coated fruits and vegetables retained their freshness longer than uncoated produce, while quince-based probiotic films showed the best mechanical, physical, morphological and bacterial viability. This is the first report of the development, characterization and production of 100% natural mucilage-based probiotic edible coatings with enhanced barrier properties for food preservation applications containing probiotics.