As sustainable production of quinoa (Chenopodium quinoa Willd.) increases and its geographic range of cultivation expands, quinoa breeding will allow use of the crop’s wide genetic diversity for cultivar improvement and for adaptation to new agroecosystems and climactic regimes. Such breeding work will require a reliable technique for crossing quinoa plants using hand emasculation. The technique described herein focuses on the isolation of small flower clusters produced low on the plant, emasculation of male flowers, and subsequent pairing of the emasculated female parent with a male parent undergoing anthesis. Various traits, such as plant color, seed color, and axil pigmentation can be used to confirm the successful production of F1 plants. The manual hybridization technology provides a significant advantage over pairing plants and relying on chance cross-pollination, and has been successfully used to generate crosses between quinoa cultivars, as well as interspecific crosses between quinoa and Chenopodium berlandieri. This technology will help pave the way for the introduction and sustainable expansion of quinoa on a global scale across a wide range of target environments and diverse farming systems.