This study investigated the organic acid and phenolic compound levels, total phenolic (TP) and antioxidant capacity (TEAC) of three miniature tomato cultivars grown on a farmer's field with three different fertilizer applications. Analysis of phenolic compound (protocatechuic, vanillic, gallic, chlorogenic, caffeic, syringic, p-coumaric and ferulic acid, rutin, quercetin, catechin and phloridzine) organic acid (citric, tartaric, malic, succinic and fumaric acid), TP and TEAC levels in fruit samples showed statistically significant (p < 0.05) differences between tomato cultivars and fertilizer applications. Rutin and chlorogenic acid were the predominant phenolic compounds found in all three cultivars. The highest rutin value (50.48 mg kg(-1) FW) was found in the Black Zebra fertilized with DAP plus organic and biochemical fertilizers and the lowest (20.52 mg kg(-1) FW) in the Black Zebra fertilized with DAP only. The highest chlorogenic acid value (63.31 mg kg(-1) FW) was found in the sweet pea currant fertilized with DAP only and the lowest (21.06 mg kg(-1) FW) in the Black Zebra fertilized with DAP plus chemical fertilizer. Citric acid content was the dominant organic acid in all three cultivars, with the highest citric acid value (6439.50 mg kg(-1) FW) found in the Sweet Pea Currant cherry tomato fertilized with DAP plus organic and biochemical fertilizers and the lowest (2435.20 mg kg(-1) FW) in the Window Box Yellow fertilized with DAP plus chemical fertilizer. Total phenolic and antioxidant levels in the window box yellow were significantly lower as compared to the Black Zebra and sweet pea currant varieties for all three fertilizer applications.