With the signing of the EU-ACP Economic Partnership Agreements (EPAs) in January 2009, Uganda as a member of the ACP, should endeavour to re-strategize itself to benefit from the opportunities such trading blocks create through increased trade. Trade is likely to increase with EPA in place and this is likely to lead to biodiversity conservation challenges amidst the need for increased production. Uganda signed and ratified the United Nations Convention on Biological Diversity (CBD) on 12th June 1992 and 8th September 1993 respectively. The objectives of CBD are the conservation of biodiversity; sustainable use of bio diversity; and the fair and equitable sharing of benefits arising from the utilization of genetic resources. Although Government has made significant progress in achieving these objectives, balancing trade and biodiversity under EPA presents challenges. In this brief we focus on fresh fruits and vegetables production and suggest some trade options that would be beneficial under EPA and also ways on how to mitigate biodiversity loss. In addition, some key policy interventions that can lead to sustainable trade in fresh fruits and vegetables are recommended.