Edible flowers are becoming popular as a nutraceutical and functional food that can contribute to human nutrition with high antioxidant molecules and mineral elements. While comparative studies between different flower species have been performed, less is known about the best agronomical practices to increase yield and nutraceutical proprieties of blooms. Silicon stimulates plant resistance against stress and promotes plant growth while non-thermal plasma (NTP) technology has been applied for the disinfection and decontamination of water, as well as for increasing plant production and quality. The application of silicon and NTP technology through nutrient solution and spraying was investigated in edible flowers given that the combination of these treatments may play a role in promoting their nutritional and nutraceutical proprieties. The treatments were applied on two varieties of Begonia cucullata Willd. (white and red flowers) to explore their effects on different flower pigmentations. Plants with red flowers showed higher nutraceutical proprieties than the white ones but yielded a lower flower number. While the NTP treatment did not improve flower yield and quality, the silicon treatment increased anthocyanins and dry weight percentage in red flowers. NTP treatment increased zinc concentration, while it decreased potassium, magnesium, and manganese, and increased silicon concentration in white flowers. The combination of silicon and NTP showed negative effects on some nutraceutical proprieties of red flowers thus highlighting that the two treatments cannot be combined in edible flower production. In conclusion, the positive effect of silicon use in edible flower production has been demonstrated while the NTP technology showed contrasting results and its use should be explored in greater depth, including a consideration of its role in biotic attack prevention and reduced chemical input.