Shallots are strategic horticultural commodities, and climatic conditions strongly influence their growth. In certain seasons, a decline in production is unavoidable, causing price increases at a consumer level and eventually contributing to the rate of inflation. The application of Good Agriculture Practices (GAP) is a strategy that can maintain and increase the productivity of shallots. This study aimed to determine the effect of applying GAP on the growth and yield of shallots in several varieties developed in North Maluku. The research was carried out in Trans Koli SP-1 Village, Oba District, Tidore Islands City, from March – June 2015. The study was arranged in a factorial, the first factor was cultivation habits (GAP and farmer habits), and the second factor was varieties (Topo-1, Topo-2, Super Philips, and Thailand), which used a Randomized Block Design with three replications. Parameters observed were plant growth, the intensity of pests and diseases, yield components and the production of shallot bulbs. The results showed no interaction between cultivation habits and varieties in all parameters, but there were significant differences between the research cultivation habits and varieties in all parameters. The Super Philips variety generally had significantly higher growth and lower intensity of armyworms than the Topo-1, Topo-2, and Thailand varieties. In terms of yield and tuber production, Super Philips and Thailand varieties have significantly higher yields than Topo-1 and Topo-2. The results of this study confirmed that the application of GAP had a better effect on growth, pest intensity, and production of shallots than farmers' habits.