Forty-six coffee companies in Indonesia have currently been certified, producing a total of 47,000 tons of certified coffee per year. This paper examines the challenges of sustainable farming system certification for coffee in Indonesia. Coffee companies were found to engage in coffee certification for a number of reasons, namely as a marketing tool, to reduce risk when prices fluctuate, to make it easier to gather coffee beans from farmers, and to receive a price premium. Among the main challenges highlighted for certification is that smallholders do not fully understand the intention and objective of certification programs, which leads to confusion in responding to complex certification criteria and indicators. The research highlights the differences in implementation of certification programs for smallholders and private and government estates. Certification for smallholders is usually conducted by traders and exporters, while for coffee estates it is conducted by plantation owners. Coffee farmers have no capability to hold certification due to constraints in cost, knowledge, networking and marketing. The authors point to the need for efficient sustainable coffee certification in Indonesia—as well as other ASEAN countries—that is cost effective and globally acceptable.