Cold plasma is a novel non-thermal technology that is still under development. Cold plasma treatment of food products induces a wide range of chemical changes in food compounds, several of which can improve nutritional quality. Understanding the chemical changes caused during plasma treatment is essential to enhance food quality and avoid the formation of undesired compounds. This investigation addressed the influence of two cold plasma technologies, glow discharge plasma and dielectric barrier discharge plasma, on the organic composition of araça-boi (Eugenia stipitata) juice, which is rich in sugars, organic and amino acids. The chemical composition of the juice was assessed by 1H nuclear magnetic resonance coupled with chemometrics. The effects of excitation frequency, processing time, and plasma flow rate were investigated. Glow discharge plasma and dielectric barrier discharge plasma application tended to decrease the concentration of glucose (33%), fructose (31%), malic acid (25%), and amino acids while increasing sucrose content (23%). Overall, plasma processing changed the juices’ alcohol, sugar, and amino acids content, primarily by reducing the concentration of cysteine (33%), alanine (42%), and methionine (43%). However, the dielectric barrier discharge plasma tended to slightly increase the amino acid content (up to 9%) when operating at 200 Hz.