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The Young Investigator Program scheme was designed from the outset to offer financial support and training opportunities to group leaders with less than four years’ experience leading a laboratory. The intention was to support both excellence and maintain a healthy geographic distribution. The scheme was first proposed to the EMBO Council in 1998, who, receiving it favorably, officially accepted it a year later and established a working group with the support of all participating countries. Council subsequently established a selection committee and carried out its first round of selections in 2001, accepting 23 candidates.

The primary allure of the program to applicants seemed from the beginning to be the Networking opportunities. The YIP program offered participants the opportunity to present their work and meet their peers at yearly meetings, access to EMBL core facilities, mentoring opportunities, and even courses for PHD students at participants’ laboratories.

In 2005 these networking opportunities expanded to include Laboratory Management Courses (now [Lab Leadership Courses]), designed to empower YIPs with skills in everything from project management to managing laboratory groups.

In 2008 the program created the Special Development Installation Grant. These were established as a Special Project of the EMBC for the purpose of supporting scientists in peripheral nations: The Czech Republic, Poland, Hungary and Estonia, and were based on and replaced the EMBO/HHMI Startup Grants. Eligibility has since grown to include Croatia, Greece, Hungary, Lithuania, Luxembourg, Montenegro, and Türkiye.

By 2011, Council noted the strength of the project, highlighting the promotion of scientists engaging in novel research topics. Through the years the prestige of the award as well as the networking opportunities has provided the greatest motivation to applicants.. YIPs currently receive a financial award of 15,000 euros in their second year, and can also apply for additional small grants of up to 10,000 euros per year. There is currently a network of over 700 YIP alumni.

EMBO’s women in science program began in the early 2000s, with a special meeting called “The Glass Ceiling for Women in the Life Sciences being held in June 2001, and Gerlind Wallon producing a position paper highlighting the issues facing women in the life sciences in December of the same year.
In 2002, EMBO established Re-Start Fellowships, the purpose of which was to support women scientists who wanted to return to the bench after having taken a break (eg. Maternity leave), with 2 year fellowships.
In 2006, the Set-Routes initiative was established. For a period of 3 years, The European Molecular Biology Laboratory (EMBL), the European Molecular Biology Organization (EMBO) and the European Organization for Particle Physics (CERN) managed an initiative to increase the visibility of women in science in education by mobilising “successful women in science, engineering and technology (SET) to go into schools and universities throughout Europe and beyond.” This project was funded by the European Commission.
In October 2008, EMBO council stated that all EMBO programmes were to keep statistics and have established rules and guidelines that highlight and address the under-representation of women in science, and in that same year the first EMBO/FEBS Women in Science awardee was chosen.
The Women in Science programme has engaged in other activities, including holding meetings, publishing reports on the issues facing women in science in scientific journals, and funding lectures by prominent women scientists.

In 1997, the first Science and Society Committee meeting was held, bringing together EMBO Members to discuss the topic of “Molecular Biology in Society”. It was decided that the defining the role that EMBO might play in science communication, both towards interested members of the public, and regarding public policy, was crucial. It was decided that a particular emphasis should be made on building interactions with secondary school teachers.

A year later Frank Gannon, then Executive Director, wrote a paper regarding Basic Research and the Future of Science Policy, again highlighting EMBO’s keen interest in leading in this sphere. In 1999 there were two joint meetings with the European Federation of Biotechnology and the European Genetics Foundation regarding controversial scientific topics, and in that same year Dr. Andrew Moore was hired to lead the Science + Society Program. Under Dr. Moore the project focused on creating events, resources, and support activities that led to better understanding of science and scientists by laypersons.

In 2002 the Science & Society Program established “Continuing Education for European Biology Teachers”, an EC Funded project Designed to provide a new layer of professional development for biology teachers through workshops, training courses, and through the creation of a resource centre. Science Communication and Science Writing prizes were also created to reward researchers for their work in communicating scientific topics to broad audiences.

Yearly stakeholder meetings were also established, bringing together scientists, philosophers, policy makers, teachers, and members of the general public to discuss controversial topics regarding scientific ethics, such as the role of genetic modification in food policy and animal testing. In the latter case EMBO published a position paper regarding its stance on the use of animals in research.

In 2006, EMBO become one of sixteen partners involved in the BioTethed project, an initiative which promoted biotechnology ethics and its interaction with other fields of science, scientists and the general public.

In 2009 EMBO organised a summer school for graduate and PHD students at EMBL, and began to be involved in the “Initiative for Science in Europe”, an organisation intended as a platform of European scientific organizations meant to promote basic science at the European level, design and implement European science policies, and advocate independent scientific advice in European policy making. The ISE was eventually realised in 2017.

In 2010 the remit of the programme changed, with its purpose now being to influence European research policy for the benefit of the scientific community, as well as analysing and advising on research-related issues. Therefore, EMBO Council decided to change the name of this programme to "Science Policy Programme”. Following this change the science policy programme was incorporate into the General Programme of the EMBC in 2012. Since then there has been a greater emphasis on ensuring the ethical conduct of members and fellows. It co-developed an Epigeum course on research integrity which became mandatory for all new fellows.

The Membership Department administers EMBO’s elected membership, the core body of the organization since its foundation in 1964. From the beginning, the EMBO Secretariat managed the nomination and election of Members. As membership grew through the 1980s and 1990s, these tasks developed into a dedicated function within the EMBO Office in Heidelberg. The department's main responsibilities are administering the annual nomination and voting process for new Members and Associate Members, acting as the point of contact for Members and communicating announcements, updates, and recognition of new elections, and keeping the official membership register and related biographical data.

The Initiative for Science in Europe (ISE) is an independent association of various research organisations and scientific groups that was founded on 25th October 2004. It was initiated to promote science in the formulation of European policy making. Its first efforts were coordinated by the European Life Sciences Forum (another organization EMBO played a crucial role in founding in 2000), but EMBO also joined as a founding member. Maria Leptin (EMBO Director 2010-2021) served as the ISE’s president and Fiona Watt (EMBO Director 2021-) currently serves on the executive committee.

With EBNIC-2 not being accepted for funding, EMBO Council decided to establish a working party to establish a strategic focus for a World Programme, analysing how much emphasis to give to different actions, different geographic areas that should be targeted, and how to interact with other national and international activities.

The World Programme was ratified by council in 2003. It initially offered 6-9 month “Medium Term” fellowships, with a focus on training, acquiring new techniques, and building relationships which should continue after the scientists’ return to their home labs. They also offered Practical courses to allow students from different continents to interact with each other and to learn new methods together, workshops to allow scientists from different countries to meet, discuss, and plan to collaborate, and plenary lectures to build the profile of European scientists internationally.

Additionally, the World Programme reached an agreement with the Chinese Academy of Sciences (CAS) to work with EMBO to establish a screening service in order to improve the flow of high-quality scientists to Europe, and in return to provide fellowships and the organisation of courses and workshops in China.

It also created a Mobility Consultancy initiative in collaboration with HFSP, the Wellcome Trust, and The World Academy of Sciences, the purpose of which was to provide information on European funding sources and grant application procedures to interested scientists outside of Europe.

In conjunction with these organisations, EMBO also coordinated a project to research information on educational opportunities, research accomplishments, and science policy in a selection of resource-constrained countries. Together they presented a meeting entitled “Promoting Life Sciences in Developing Countries”, bringing together representatives of major international organisations supporting the sciences in resource-constrained countries, and published a report off the back of this meeting.

In 2008 council decided to establish a working party to advise on future strategies related to developing a policy strategy to inform EMBO’s relationships with Non-European countries, and a year later the program was renamed “EMBO Global Exchange Programme”. The purpose was not to teach basic research, but instead to establish high-level scientific interactions/partnerships with countries where good science and scientific infrastructure had already been established. A committee was established to oversee its activities. In 2012 the name was changed once again, this time to “Global Activities”.

In 2005 the EMBC began to formalise its relationships with countries outside of the European area, initiating a cooperation status with South Africa, which expired in 2016. Following this, the EMBC established its first full cooperation agreement with Singapore in 2011, with Singapore subsequently become EMBO’s first Associate Member State in 2015. India became an Associate Member State a year later in 2016. Taiwan entered a cooperation agreement with EMBO in 2012, Chile signed one in 2018, and the Japan Science and Technology Agency signed one in 2023.