The study assessed producers’ awareness and perceptions of territorial-based qualities and the economic potential of two potential origin-based geographical indications in two semi-arid counties in Kenya. Protection of the origin products as geographical indications is presented as an option for ecosystem approach in managing fragile semi-arid regions while providing producers economic incentives and social inclusion; key components of green growth. Factor analysis was conducted on Likert scale perception questions administered to producers of goats (Baringo) and mangoes (Makueni). The producers were aware of the uniqueness of their products and its geographical source. The resultant factors reveal the importance of public policies, institutions, market access and public sector actors as important to producers’ perception of the success of protecting their products as geographical indications. Clustering revealed producer heterogeneity in their perceptions of protecting their respective products as geographical indications. The constitution of the clusters was significantly different based on the number of years the producers had practiced farming in the region, their awareness of the uniqueness of their goats, income received from goat production and institutional factors. Enhanced collective action for both goats and mangoes in the semi-arid regions would ensure collective reputation in the product presented to the market. The producers’ perceptions emphasise geographical indications as a marketing tool rather than an environmental tool, agreeing with Principle 4 of the ecosystem approach on managing ecosystem in an economic context.