The quality-oriented fruit production in well-controlled enclosed hydroponic systems has been greatly enhanced by the technology of precision agriculture. Over-fertilisation has been commonly applied to the traditional hydroponic culture of fruit crops, without considering different nutrient demands during development. Adjusting the nutrient formulations depending on crop developmental stages could enable efficient fertilisation to increase yield quality. In this study, N-reduced and K-modified nutrient solutions were applied for a two-step nutrient manipulation experiment, to improve the fruit quality (Experiment I) and optimise the fertilisation schemes (Experiment II) of hydroponic netted melon (Cucumis melo L. var. reticulatus). The N-reduced and K-modified treatments, before fruiting stage in Experiment I, obtained higher fruit quality with increased fruit weight, dry matter ratio, flesh thickness, and total soluble solids. In Experiment II, fruits cultured under treatment II-3 (applied with 100-75-100% N and 100-125-75% K during VG-PYF-FEM) had the highest overall preferences, with ‘rich’ aroma, ‘dense’ texture, and ‘perfect’ sweetness, compared to all other experimental treatments. Our study successfully improved the fertilisation schemes for a hydroponic netted melon with precise N- and K-nutrient formulations specific to different developmental stages. Our study promotes the future advancement of precise fertilisation to improve fruit quality and reduce environmental pollution from farming activities.