The formation of green trihydroxy benzacridine (TBA) derivatives when chlorogenic acid (CGA) quinones and amino acids react can be visually unappealing in some applications where CGA containing ingredients are used. Cysteine was studied as an amino acid anti-greening strategy, because cysteine-CGA conjugates are colorless. Buffered CGA: lysine: cysteine solutions at pH 8.0 and 9.0 were prepared and incubated for a maximum of 48 h at ambient temperature. Color intensity was periodically monitored using a UV-Vis spectrophotometer. Quantification and identification of conjugate formation were conducted by HPLC and LC-MS, while Antioxidant capacity was assessed by Trolox Equivalent Antioxidant Capacity and Folin-Ciocalteu reagent reducing capacity assays. More intense greening was detected at higher pH. Lysyl amine- CGA conjugates were identified as the predominant precursor of green TBA. Concentration-dependent cysteine inhibition of CGA-lysine greening was primarily by redox diphenol regeneration when pH was below cysteinyl thiol pKa 8.3 while primarily by forming cysteinyl-CGA conjugates when pH was above 8.3. Visible greening was fully inhibited with a cysteine: lysine 1:1 molar ratio in pH 9 CGA: Lys: Cys solutions, indicating that cysteinyl thiol was a stronger nucleophile than ε-lysyl amine to react with CGA o-quinones. Mono- and di-cysteine-CGA conjugates contributed to antioxidant capacity. Cysteine concentration, pH and incubation time all significantly affected color intensities and antioxidant capacity (p