BACKGROUND: Most people with febrile illness are treated in the private drug retail sector. Ghana was among nine countries piloting the Global Fund Affordable Medicines Facility - malaria (AMFm). AMFm aimed to: increase artemisinin combination therapy (ACT) affordability; increase ACT availability; increase ACT use; and 'crowd out' artemisinin monotherapies. METHODS: Three censuses were carried out 2 months before (2010), 2 months after and 2.5 years after (2013) the first co-paid ACTs to assess changes in antimalarial (AM) availability and price in private retail shops in a Ghanaian rural district to assess the sustainability of the initial gains. Supply, stock-out and cost were explored. RESULTS: Of 62 shops in the district, 56 participated with 398, 388 and 442 brands of AMs in the shops during the 3 censuses. The proportion of ACTs increased over the period while monotherapies reduced. Herbal-based AM preparations comprised 40-45% of AMs in stock with minimal variation over the period. ACTs were the most sold AM type for all ages but overall buying and selling prices of Quality Assured-ACTs increased by 40-100%. CONCLUSIONS: Initial gains in ACT availability were sustained, but not improved on 2.5 years after AMFm. Widespread availability of unproven herbal medicines is a concern; AMFm had little impact on this.