Since 2006, EU cooperation with Botswana shifted from the traditional "project approach" to "budget support". Up to 85% of EU assistance is now channeled through the Government budget in the form of annual disbursements, based on the achievement of agreed educational and HIV prevention results. This performance-based approach, where assistance is provided to help government deliver on the targets that it has itself set, reflects a maturing relationship between the EU and Botswana characterized in particular by EU's confidence in Botswana's development plans and public finance management systems.

The EU is the most important trading partner for the SADC region. The EU absorbs around 40 percent of SADC exports which also corresponds to SADC imports. In order to improve the competitiveness of ACP countries, the Cotonou Agreement provides for a new type of regional trading arrangement known as Economic Partnership Agreements (EPAs), currently negotiated between inter alia EU and SADC. A number of trade related projects have been financed by the EU over the years. The SADC Regional Indicative Programme (RIP) for 2008-2013 support from the EU earmarks an amount of €116 million in support of regional economic and regional political integration, which is to be delivered through implementation of Contribution Agreements with the SADC Secretariat.