The EU and Indonesia have entered into a Partnership and Cooperation Agreement (PCA). The PCA covers areas such as trade, environment, energy, education, science and technology, migration and counter-terrorism. Thriving trade links, democracy and human rights, action on climate change and terrorism at home and abroad and expanding people-to-people links are all key areas of focus. Both the EU and Indonesia have historically been committed to peace and stability in the country, one notable feature being the EU's support for the Aceh peace process.

In April 2016, EU and Indonesian leaders announced the conclusion of pre-negotiation discussions (scoping) designed to enable the launch of negotiations for a so-called Comprehensive Economic Partnership Agreement (CEPA), more commonly known as a Free-Trade Agreement (FTA). If realised, the CEPA between the EU and Indonesia will be a trade agreement with a potentially impressive scale, creating a combined market of more than 750 million consumers. The economies of the EU and Indonesia are quite complementary as regards trade in goods and services, and therefore the potential benefits of concluding a CEPA are proportionally larger. An FTA between the EU and Indonesia would provide for a more stable, balanced and long-term framework to enhance trade and investment relations between the EU and Indonesia. A study published by the reputable Indonesian institute, the CSIS, in May 2015, assessed the potential gains from concluding a CEPA between the EU and Indonesia. If the CEPA manages to eliminate tariffs on all goods, the annual quantities that the EU will import from Indonesia could increase by 5.4 % when compared to their current value — an increase equivalent to an additional USD 1.1 billion. In addition to pure trade creation effects, the study also points to other potential benefits.

The EU is one of the largest partners supporting education in Indonesia. The EU has promoted education reforms through three main initiatives under the Education Sector Support Programme (ESSP). First, running from 2008 to 2017, the EU provides direct budget support to the government to increase access to primary education and improve the quality, relevance and governance of education more broadly. Second, the Analytical Capacity and Development Partnership has carried out 40 evidence-based policy studies addressing, among other things, gender, early childhood development, student assessment systems, improved teaching and learning techniques, and a roadmap for a qualifications framework. Third, the Minimum Service Standards Capacity Development Programme supports the implementation of Minimum Service Standards in basic education. It addresses quality, governance and regional disparities in education with concrete actions such as teacher training and the provision of school books.

In addition to these projects, the EU also supports higher education in Indonesia. Through the Erasmus+ programme, the EU awarded over 100 scholarships for Indonesian students to study in Europe in 2015. Today around 9 000 Indonesian students are studying in Europe, of which 1 600 have received scholarships from the EU and its countries. Events such as the European Higher Education Fair (EHEF) are valuable opportunities for students to find out what's available. 

The EU supports the Indonesian government's priorities designed to support good governance, combat corruption, improve justice and law enforcement, promote greater respect for human rights and combat trans-national crime. Other work by the EU here has focused on training judges and law enforcement. To help improve government revenue administration and sound public financial management, the EU has contributed €10 million towards the €21 million Public Finance Management Multi-Donor programme, phase II. Similarly, the €10 million SUSTAIN project is working to improve the transparency, integrity and accountability of the judiciary and the quality of justice services for all citizens. Furthermore, this is complemented by a four-year Improving Efficiency, Transparency and Accountability in Public Procurement project, now in its second phase and supported by the EU with €600 000, which aims to enhance integrity in public procurement in seven target local governments. In the past, the EU also provided a €12 million programme that supported the institutional strengthening of the Corruption Eradication Commission (KPK), the Indonesian National Police (INP) and the Jakarta Centre for Law Enforcement Cooperation (JCLEC).

The EU is one of the main development actors promoting initiatives that protect the environment, the sustainable management of Indonesia's rich rainforests and the fight against climate change.

In 2015, at the Paris climate conference (COP21), Indonesia committed to reducing emissions by 29 % by 2030 as compared to the 'business as usual' scenario. Protecting the environment and addressing global climate change have become central in EU-Indonesia development cooperation activities. Both parties recognise that reducing greenhouse gas emissions is key to countering global warming.

In 2013, the EU and Indonesia signed a Voluntary Partnership Agreement (VPA) to improve forest governance and promote trade in legal timber from Indonesia to the EU. Indonesia, with the help of civil society, initiated and developed a system giving its timber access to the European market.

Elsewhere, the EU's Forest Law Enforcement Governance and Trade (FLEGT) Action Plan has helped enable Indonesia to develop one of the most advanced Timber Legality Assurance Systems in the world (the SVLK or Sistem Verifikasi Legalitas Kayu).

The EU also supports Indonesia’s national climate change response via a €15 million Climate Change programme, notably supporting the Aceh and Papua provinces in their efforts towards low-emission development planning.

A change to sustainable consumption and production is supported by the EU and Indonesia. To encourage this, the EU has been implementing the SWITCH-Asia programme in 16 Asian countries, including Indonesia, since 2007.