Purpose This exploratory study aims to identify and prioritize key sustainable innovation challenges faced by family-owned businesses in the wine ecosystem. It also explores whether the criticality of these challenges differed pre- and post-COVID-19 by comparing the prioritization of these challenges at these two times. Design/methodology/approach Three methodologies were used. First, a systematic literature review identified the key sustainable innovation challenges in the wine ecosystem, which were then summarized into macro-categories (macro-challenges). Second, a panel of experts validated these challenges. Finally, the best-worst method was used using 40 qualitative interviews to prioritize the most critical challenges in two alternative scenarios to explore potential changes in challenge criticality following COVID-19. Findings This study provides evidence that the primary challenge to sustainable innovation (i.e. constraints on businesses because of limited financial resources) was the same pre- and post-COVID-19. In contrast, although the challenge associated with knowledge sharing was identified as a key strategy of wine ecosystem actors, particularly in recent years, it was the least critical factor at both times. Originality/value This exploratory study extends the conceptual boundaries of sustainable innovation by introducing it to the wine ecosystem. It establishes a practical agenda for small and medium-sized enterprises to enable managers who are constrained by limited resources to prioritize challenges. This agenda outlines a path to identifying competitive strategies. This path can also be followed by a range of stakeholders within this ecosystem to achieve resilience and define medium-to-long-term strategies. Furthermore, policymakers and governments can follow this path to formulate more targeted investment management plans and policies, thereby supporting sustainable economic growth in this key sector for many countries.