Purpose: The aim of the research was to propose probable scenarios for the year 2030 for the cocoa value chain in the department of Antioquia (Colombia), based on functional approach to analysing territorial innovation systems (TIS). Methodology: TIS in the cocoa value chain was analysed by comparing two rural municipalities as case studies, where different actors respectively participated. Prospective analysis approach, Delphi method, MICMAC program and morphological analysis were combined for the construction of scenarios. Findings: Case study comparison indicates that analysis at the territorial level is an appropriate perspective to identify key aspects of the TIS functions that lead to different scenarios for promoting local innovation in agri-food value chains. The results provide specific scenarios including short-, medium- and long-term strategies for the promotion of territorial innovation systems. Practical implications: This approach has the potential for multiple heterogeneous TIS actors to explore different innovation pathways and prospective scenarios that contribute to action planning to reduce uncertainty and promote innovation in TIS. Theoretical implications: This study contributes with a new way of approaching the functions of TIS, where dynamics that occur in the local geography are highlighted. Also based on the prospective analysis, scenarios are configured that arise from a set of aspects analysed by local and external actors of the territories. Originality/value: The study generates important knowledge about TIS and the functional approach regarding the design of prospective scenarios to promote innovation in agri-food value chains.