Cocoa is important for the economy and rural development of Ghana. However, small-scale cocoa production is the leading agricultural product driver of deforestation in Ghana. Uncertain tree tenure disincentivizes farmers to retain and nurture trees on their farms. There is therefore the call for structures that promote tree retention and management within cocoa farming. We examined tenure barriers and governance for tree resources on cocoa farms. Data was collected from 200 cocoa farmers from two regions using multistage sampling technique. Information was gathered on tree ownership and fate of tree resources on cocoa farms, tree felling permit acquisition and associated challenges and illegal logging and compensation payments on cocoa farms. Results suggest 62.2% of farmers own trees on their farms. However, these farmers may or may not have ownership rights over the trees depending on the ownership of their farmlands. More than half of the farmers indicated they require felling permits to harvest trees on their farms, indicative of the awareness of established tree harvesting procedures. Seventy percent of the farmers have never experienced illegal logging on their farms. There is however the need to educate the remaining 30% on their rights and build their compensation negotiation powers for destructions to their cocoa crops. This study has highlighted ownership and governance issues with cocoa farming and it is important for the sustainability of on-farm tree resources and Ghana’s forest at large.