‘Lemonato’ is a Greek peach melting-flesh white-flesh cultivar with high nutritional value highly appreciated by the consumers. This study aimed to evaluate the effect of pre-harvest foliar calcium application on fruit quality, primary metabolite profile, antioxidant activity, total phenolic content, and phenolic profile of the ‘Lemonato’ peach, clone ‘Stamatis’. The experiment was conducted for two years, 2019 and 2020, in two commercial orchards at Kato Lehonia and Agios Vlasios regions, central Greece, where the ‘Lemonato’ clone ‘Stamatis’ is traditionally cultivated. The treatments were organic calcium (Ca), calcium–silicate in nanoparticles (Ca–Si), and calcium chloride (CaCl2). Foliar application of the different Ca formulations, commonly used as a horticultural practice, were not effective at improving the fruit quality characteristics in this clone, which is characterized by fruit softening during ripening. The study revealed the sugars and organic acid composition and phenolic profile of the ‘Lemonato’ peach, clone ‘Stamatis’. Peach fruit quality, primary metabolites, and phenolic compounds of the two orchards showed a different response to organic Ca and Ca–Si, indicating that genetic or environmental factors may also be involved. A higher concentration of organic Ca and CaCl2 increased the peach fruit phenolic compounds content and the total antioxidant activity, improving the fruit nutritional quality.