Edible flowers are becoming increasingly popular as food products, since they give aroma, color, and visual appeal and are also health-promoting compounds. However, they are a highly perishable product, thus post-harvest technologies are needed to extend their marketability. In this study, active (N2: 100%) and passive modified atmosphere packaging (MAP) technologies were applied to three edible flower species, namely Begonia grandiflora ‘Viking’, Tropaeolum majus, and Viola cornuta, stored at 4 °C. Even if the flowers’ quality decay occurred differently according to the species, active MAP better maintained petal colors and slowed down the edible flowers’ decay than passive MAP by decreasing flower respiration in all three species and sugars consumption in begonia; there was less weight loss in nasturtium, and better preserved total phenolic content in begonia and viola. Coupling cold storage with active MAP can be an effective method to extend edible flowers’ post-harvest life.