The adverse effect of Persistent Organic Pollutants (POPs) which includes endocrin disruptions, cancer, heart disease, impairment of the reproductive system, diabetes and obesity, among others, are very well documented. The Stockholm Convention on Persistent Organic Pollutants (182 state parties) restricts and prohibits the production, use, emission, import and export of persistent organic pollutants. Nevertheless, implementation of the Stockholm Convention by a country may require some adjustment in its national legal system. Indonesia ratified the Stockholm Convention in 2009; however, its implementation has not been smooth. This article analyses Indonesia’s environmental and other relevant legislation and outlines the challenges that need immediate resolution so that the Stockholm Convention can be fully implemented. This article contends that there are gaps within the Indonesian legal framework which need to be addressed, namely: (i) redefinition and recategorisation of regulated objects beyond ‘substances’ so that it covers ‘articles’ and ‘mixtures’ (ii) ways to cope with a growing list of POPs and (iii) gaps in the regulation of POPs life cycle, from production to import, use, registration, storage, disposal and ‘unintentional release’ as well as (iv) the need for new environmental and product standards.