Homegardens have long been recognized for contributing to household food security, nutritional status, and ecological sustainability in especially poor, rural areas in low-income countries. However, as markets and policies drive the commercialization of food and farming systems, and of rural livelihoods in general, it becomes increasingly difficult for small-holder farmers to maintain homegarden plots. Rather than autonomous spaces to grow food for self-consumption, farmers are transforming the land around their dwellings into an income-generating space by planting commercial crops for sale in urban and processing markets. The objective of this study was to examine homegarden commercialization in the Upper Citarum Watershed of West Java, Indonesia, and its effects on food security and food sovereignty. We employed a mixed-method approach to survey 81 village households involved in agricultural production. For quantitative analysis, we calculated a “homegarden commercialization index,” and developed indicator frameworks to examine relationships between commercialization, household food security, and food-related decision-making. Accompanied by insights from qualitative interviews, our results show that homegardens are highly commercialized, which contributes to the spread of monocultural production in the region. We argue that homegardens should be included and supported in food, agricultural, health, environmental, and rural development policy, in Indonesia and generally.