•Cysteine improves red beet bioactive compounds.•Betalains content is favored by cysteine application.•Cysteine does not decrease polyphenol oxidase activity in fresh-cut red beet.•Cysteine favors the shikimate pathway product concentration in fresh-cut red beet. This study investigated the effectiveness of cysteine in conservation of bioactive compounds and the antioxidant capacity of minimally processed red beet. After red beet minimal processing increasing cysteine concentrations were applied, corresponding to control, 2 mM, 4 mM, 8 mM and 16 mM. Assay was performed over 15 d to evaluate the polyphenols, betalains, antioxidant capacity and enzymatic activity of polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL). Cysteine enhanced the gallic acid, caffeic acid, chlorogenic acid, kaempferol and betalain contents until 6 d of storage. Subsequently, dosages of cysteine above 4 mM maintained gallic acid, kaempferol and betalains contents. Cysteine appears to influence the phenylpropanoid pathway, favoring the accumulation of polyphenols and betalains. In red beet, cysteine did not inhibit PPO activity but enhanced PAL activity. Betalains contribute more than phenolics to the antioxidant capacity, and their relationship with cysteine has not been thoroughly elucidated to date.