The flowering of shallot is influenced by low temperature and difference temperature between day and night. In Indonesia, to flowering shallot in low temperature are possible by planting in highlands. Because of climate change, the temperature difference in the highlands is very pronounced. This study aimed to determine the percentage of flowering and True Shallot Seed (TSS) production of three shallot varieties grown in the highlands. The research was conducted at Pancot Village, Tawangmangu, Karanganyar, Indonesia. The elevation of research site was 1, 300 m asl. The research design used was Split Plot with three replications. The main plot was variety: Bali Karet, Bali Lancur, and Bima Brebes. The subplot was fertilizers composition (Manure, ZA, SP36, KCl) and gibberellins: farmer’s dose (100% Inorganic and Organic) (P1G0), 100% Inorganic and Organic + Gibberellin 50ppm (P2G1), 50% Inorganic and 150% Organic (P3G0), 50% Inorganic and 150% Organic + Gibberellin 50ppm (P4G1), 200% Organic (P5G0), 200% Organic + Gibberellin 50ppm (P6G1). The results showed that fertilizer composition + gibberellins and varieties did not have significant effect on percentage of flowering, number of flowers and percentage of TSS formation. Fertilizer composition + gibberellins just influenced the number of TSS per stalks. Bima Brebes variety with P6G1 was able to flowering at 65 DAP with the flowering percentage reaching 88.87%.