The aim of this study was to investigate the effect of phosphorus application in the form of polyphosphates on the yield and quality of sweet pepper fruits grown with LED (light-emitting diodes) assimilation lighting. Phosphorus is absorbed by the root system of plants mainly in the form of orthophosphates ions. The availability of phosphorus depends, among other things, on the pH of the substrate and the temperature. Two cultivars of sweet pepper with red fruits were tested in hydroponic cultivation on a mineral wool substrate. The plants were fertilized with one of three schedules, each of the same concentration of components, but differing only in the form of the applied phosphorus: polyphosphates (PP) and orthophosphates (OP). In the experiment, stem length extensions and number of leaves, chlorophyll concentration in leaves and fluorescence of the chlorophyll in a leaf were measured. The number and weight of fruits in total as well as marketable and non-commercial fruits with symptoms of dry rot (BER—blossom end rot) were studied. The concentration of dry matter and selected chemical components in fruits were examined and the sensory quality of fruits was evaluated using the QDA (Quantitative Description Analysis) method. The nutrient status of the pepper plants was also examined. Polyphosphates used in the medium increase the activity of photosynthetic apparatus of leaves and have a positive effect on the share of marketable yield of the total yield in the cultivar susceptible to BER. Fertigation in hydroponic cultivation with medium containing 30% phosphorus in the form of polyphosphates increased the uptake of calcium in pepper plants growing with LED lighting. The pepper cultivars tested differ in, among other things, the susceptibility to BER and the quality attributes of the fruit.