Despite the acknowledged importance of innovation for enterprises’ sustainable development, in comparison to technological innovation, research on market-based innovation is still in its nascent stage. It is unclear what factors will predict market-based innovation and how market-based innovation boosts innovation performance. Therefore, based on an adaptive marketing capabilities perspective and drawing on insights from the organizational ambidexterity literature, this study explored the relationships among enterprises’ marketing capabilities, market-based innovation and innovation performance. Data collected from 237 manufacturing enterprises in China were analyzed using hierarchical regression analysis and bootstrapping methods. The results showed that: (1) Marketing capabilities and market-based innovation activities are both ambidextrous. Specifically, marketing capabilities include marketing exploration capabilities and marketing exploitation capabilities, and market-based innovation includes exploratory market-based innovation and exploitative market-based innovation. (2) Ambidextrous marketing capabilities can enhance innovation performance significantly, with ambidextrous market-based innovation playing a partial mediating role in this relationship. Specifically, marketing exploration capabilities affect innovation performance through the partial mediating role of exploratory market-based innovation, whereas marketing exploitation capabilities affect innovation performance through the partial mediating role of exploitative market-based innovation. (3) Exploratory market-based innovation negatively moderates the relationship between exploitative market-based innovation and innovation performance, and exploitative market-based innovation also exerts a negative moderating effect on the exploratory market-based innovation–innovation performance association. These findings complement and enrich the ambidextrous capability (innovation) theory, helping manufacturing enterprises to better understand and deploy ambidexterity, and hence to achieve sustainability.