New aquaculture systems are emerging in new contexts around the world in part due to aquaculture’s perceived development benefits. However, linkages between aquaculture and food security in these systems are unclear. This study investigated the impact of emerging small-scale, business-oriented fish culture in central Bolivia on the food security and dietary diversity of aquaculture producers (n = 40) and workers (n = 26) in the value chain and compared them to local non-aquaculture farmers (n = 40). Three pathways were investigated: fish consumption, household income, and women’s participation. Food insecurity was widespread and did not vary in a statistically significant way between groups, but a trend toward greater food security amongst aquaculture producers was observed. Dietary diversity was highly homogenous, with the notable exception of high fish consumption amongst producers. Aquaculture was related to higher income, and income has a modest positive effect on food security for aquaculturists and non-aquaculture farmers, but not aquaculture value chain workers. Income did not have an effect on dietary diversity. Women’s involvement in aquaculture was correlated positively to productivity, profitability, and size of operation, while male-only aquaculture was negatively correlated to these. The value chain generated employment, especially for women, but average wages were higher for men. The research provides important insight into aquaculture-food security linkages by showing that the introduction of small-scale business-oriented aquaculture systems can provide nutritious products for regional consumption and can have positive effects on food security but is not sufficient to change local dietary preferences more broadly.