The world has seen rapid growth of preferential trade and investment agreements (PTAs) that, by definition, aim to go beyond the existing WTO obligations of the parties. With this growth comes the danger of incompatible obligations as these PTAs overlap within a country. This study examines the sources of overlap in various PTAs and the compliance costs that PTAs may create for a developing country, with a special focus on the agricultural realm. Examining the reality of divergent SPS standards, we conclude that better-targeted “Aid for Trade” and regulatory streamlining within the EU can help to mitigate compliance costs in developing countries. Additionally, involvement of the private sector at an earlier stage in PTA negotiations may also help to clarify compliance costs and build their mitigation into the agreements.