The optimal fertilizer concentration for Mentha plants is contingent on the growing systems and harvest time, serving as operational solutions to control and enhance quality and yield. This study aimed to determine the effects of three macronutrients concentration in hydroponic nutrient solution (HNS) during three harvest times on the growth, quality, yield, and shelf life of three mint species (M. spicata L. var. viridis (MV); M. piperita L. (MP); M. spicata L. var. rubra (MR)) grown in a New Growing System (NGS®). Total dry matter (DM), nitrate (NO3−), phosphate (PO43−), and calcium carbonate (CaCO3) concentrations were increased with the addition of higher levels of nutrient fertilization in three species. When the ion concentration of the HNS was increased, total fresh yield decreased. The highest total bacterial count (TBC) was obtained in MR species in the three harvests in all the levels of HNS. The lowest browning potential (BP) and soluble o-quinone (So-Q) levels were observed at second harvest in the MR species with the application of one of the two HNS high in nitrogen (N). In conclusion, the combination of optimal HNS ion concentration and appropriate species is considered essential to obtain suitable yield, quality, and ensure shelf life of mint.