Non-thermal plasma (NTP) appears a promising strategy for supporting crop protection, increasing yield and quality, and promoting environmental safety through a decrease in chemical use. However, very few NTP applications on containerized crops are reported under operational growing conditions and in combination with eco-friendly growing media and fertigation management. In this work, NTP technology is applied to the nutrient solution used for the production of gerbera plants grown in peat or green compost, as an alternative substrate to peat, and with standard or low fertilization. NTP treatment promotes fresh leaf and flower biomass production in plants grown in peat and nutrient adsorption in those grown in both substrates, except for Fe, while decreasing dry plant matter. However, it causes a decrease in the leaf and flower biomasses of plants grown in compost, showing a substrate-dependent effect under a low fertilization regime. In general, the limitation in compost was probably caused by the high-substrate alkalinization that commonly interferes with gerbera growth. Under low fertilization, a reduction in the photosynthetic capacity further penalizes plant growth in compost. A lower level of fertilization also decreases gerbera quality, highlighting that Ca, Mg, Mn, and Fe could be reduced with respect to standard fertilization.