A cultivated mushroom species, Pleurotus citrinopileatus, is becoming increasingly popular thanks to its attractive colour and medicinal properties. In this study, P. citrinopileatus was grown in a cultivation medium enriched with wheat bran (WB), thymus post-extraction waste (TPEW) and pumpkin post-extraction waste (PPEW) products. The study showed that the post-extraction wastes are a crucial factor determining the accumulation of minerals, the content/profile of low-molecular-weight organic acids (LMWOAs) and phenolic compounds in fruit bodies, thereby increasing their nutritional value. The use of the waste materials significantly increased LMWOAs contents. The sum of LMWOAs under all cultivation mediums increased, especially quinic, malic and citric acids under the 20% PPEW, 25 and 50% TPEW addition. Total phenolic content, phenolic content, as well as the composition and scavenging effect on DPPH radicals, were strongly dependent on the used substrate. The control variant was poor in phenolic compounds, while the supplementation increased the contents and diversity of these metabolites. In the control, only four phenolic compounds were quantified (chlorogenic, gallic, syringic and vanillic acids), while in the supplemented substrates up to 14 different phenolic compounds (caffeic, chlorogenic, p-coumaric, 2,5-dihydroxybenzoic acid, ferulic, gallic, protocatechuic, salicylic, sinapic, syringic, trans-cinnamic and vanillic acids, catechin and rutin).