Shallots are a vegetable commodity that is considered used as a spice in cooking, so the need of the consumer is high. To supply this high consumption is needed increased productivity. Productivity can be increased by using varieties suitable for the growing environment, quality seeds, and proper fertilization. One of the uses of quality seeds is from seeds, but to obtain high production from seeds, appropriate fertilization is necessary. The goal of the study is to establish the liquid organic fertilizers type and the shallot variety from true shallot seed (TSS) can increase yield in the highlands. This research was conducted in IP2TP Berastagi, with a height of 1340 m asl and andisol. This study was conducted from May to September 2018. The Randomized Block Design factorial was used as a research design with 3 replications. The first factor is liquid organic fertilizer (LOF): Without LOF, Rabbit manure LOF, Fish fertilizer LOF, and Fish LOF. The second factor is shallot varieties from seed: Bima, Trisula, and Tuktuk. The results showed that the growth of shallots had no effect in giving liquid organic fertilizer to the seeds. The Trisula shallot variety can adapt to grow and produce well in highlands, while the Tuk-tuk variety is only adapted for growth and the Bima variety is less adaptive for growth and yield. The Trisula shallot variety with rabbit manure liquid organic fertilizer was able to give the best results compared to other treatment combinations (increased the yield by 13.70 – 65.10%.). The Trisula variety can be recommended for planting in highlands by utilizing LOF of rabbit manure.