Innovation is a highly sought-after but also highly complex phenomenon that thrives in ecosystems where human capital, knowledge, infrastructure, investment, trade, and institutions converge. Research and Innovation (R&I) do not occur in isolation; they are fueled by a "critical mass" of collaborative actors that allow ideas to scale into economic impact. However, this capacity is unevenly distributed worldwide and in the European Union as well.

We know well that the core aim of the EU Cohesion policy (CP) is to reduce economic, social, and territorial disparities within the Union. As we look deeper into it, the Cohesion policy’s very first objective (PO1) specifically targets "a more competitive and more innovative Europe" through the instruments at its disposal. This leads to natural convergence of Cohesion policy goals with the much broader architecture of European development, and when it comes to innovation, alignment with the Horizon Europe programme in particular.

​This alignment has not gone unnoticed and is underutilised. Since experts and policymakers started analysing the CP programming period of 2014-2020, a clear vision of building complementarities with the Horizon Europe programme has emerged, to “foster sustainable and smart regional economic development, while at the same time improving the EU’s innovation ecosystem overall and making it better at responding to key societal challenges and developing key strategic value chains,” as it was noted in the Commission Notice 2022/C 421/03.

Simply put, Horizon Europe and EU Cohesion Policy already support different parts of the same innovation process. By combining the two, countries and regions can use EU money more effectively, help weaker regions join European research networks, and avoid situations where different EU programmes fund overlapping activities separately instead of reinforcing each other. So, for its 2021-2027 programming period, Horizon Europe was already envisioned as the programme that “shall thus maximise Union added value by focusing on objectives and activities that cannot be effectively realised by Member States acting alone, but in cooperation.”

So, in this article, we examine the synergies between Cohesion Policy and Horizon Europe to see how they support regional development and innovation in the EU, while also serving as an exercise in converging complex policies to achieve a broader goal, one that neither could attain independently.

The material is developed by the Swiss–Ukrainian project UCORD, in cooperation with the European Association of Development Agencies (EURADA) and the Decentralization portal. The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views of the Swiss Agency for Development and Cooperation, or NIRAS Sweden AB.

Explaining Horizon Europe and Key Concepts in Connection with EU Cohesion Policy

Horizon Europe (HE) is the EU’s key funding programme for research and innovation for the 2021-2027 period. With a budget of €93.5 billion and across its four pillars, HE supports scientific excellence, technological development, industrial competitiveness, and solutions to major societal challenges such as climate change, digital transformation, public health, and energy security.

In practical terms, Horizon Europe finances collaborative research projects, innovation actions, researcher mobility, research infrastructures, and the commercialisation of new technologies. Universities, research organisations, companies, public authorities, NGOs, and regional actors from across Europe can participate in the programme, as described in Regulation (EU) 2021/695 — the key regulation on Horizon Europe.

Horizon Europe is a practical part of the EU's broader ambition of building a competitive, knowledge-driven economy where research results can move efficiently from laboratories to markets and society. An important part of that is the European Research Area (ERA), also in part supported by Horizon Europe. Established in 2000 according to the objectives of Article 179 of the Treaty on the Functioning of the EU, the European Research Area refers to the EU’s vision of creating a “single market” for research and innovation. The idea is comparable to the EU single market for goods and services: researchers, scientific knowledge, technologies, and innovation should circulate freely across borders.

In this sense, the ERA aims to ensure that research excellence is not isolated within national systems, but connected across Europe. It promotes cooperation between universities, research centres, businesses, and governments while encouraging shared standards, open science practices, research mobility, and coordinated investment in strategic priorities.

Closely connected to the ERA is the European Innovation Ecosystems (EIE) programme, which seeks to connect startups, scale-ups, investors, universities, regional authorities, innovation agencies, and industry clusters into more integrated European innovation networks. EIE is part of Horizon Europe and it contributes to the New European Innovation Agenda by scaling up deep tech innovations, boosting innovation procurement, and connecting various European innovation ecosystems. The EIE programme notably supports the Regional Innovation Valleys (RIVs) initiative, which connects regions with higher innovation performances and those with lower innovation capacity to “build on strategic areas of regional strength and specialisation (defined in their smart specialisation strategies)”.

Having covered Smart Specialisation Strategies (S3) in our previous materials, here we can see how interconnected they are with multiple EU policy goals. As a place-based innovation policy approach, S3 embodies a simple idea, in this case, at the crossroads of Horizon Europe and EU Cohesion Policy: rather than attempting to develop excellence in every possible field, regions are encouraged to identify their strongest assets, capabilities, and economic potential, and then concentrate investment in selected priority domains. Cohesion Policy funding can help regions build research capacity, innovation infrastructure, and institutional readiness, while Horizon Europe can connect those regional capacities to European-level research networks and excellence-driven projects.

However, before we jump to outlining concrete synergies, proposed by the EU, one key institutional actor needs to be mentioned. Managing Authorities (MAs) are national or regional public bodies responsible for administering EU Cohesion Policy funds, including programmes financed through the European Regional Development Fund (ERDF).

Their responsibilities include efficient management and implementation of operational programmes, with key tasks like transmitting implementation data, ensuring funded activities meet criteria, checking co-financed products and services, recording operational data, and evaluating program performance. Importantly, with the introduction of Commission Notice 2022/C 421/03, Managing Authorities have also started to play a strategic coordination role between regional development priorities and broader EU innovation objectives: “it is for the MAs to decide whether or not to use synergy mechanisms”, states the Notice. We’ll outline the synergies in the next chapter.

Types of Synergies

The Commission Notice 2022/C 421/03, published in November 2022, offers guidance on key synergies between Horizon Europe and programmes of the European Regional Development Fund, which constitute Cohesion policy funds in this context. Further on, we will quote the Notice only, to describe and explain the very practical ways the funding complementarities are built.

Seal of Excellence

The Seal of Excellence is a quality label awarded to high-scoring HE proposals that cannot be funded due to budget constraints. It signals to ERDF programmes, national funders, or private investors that a project is worth supporting – “the Seal of Excellence indicates that a project might be a good candidate for receiving support from other EU or national sources of funding”.

Managing Authorities (MAs), exercising their strategic coordination role between regional development priorities and broader EU innovation objectives, can use a simplified selection process for these projects. They should rely on HE’s evaluation while checking compliance with ERDF programme objectives and enabling conditions. State aid rules allow ERDF to fund these projects at the same rate and eligible costs as HE, without prior notification to the Commission.

Transfers from ERDF to Horizon Europe

Under Article 26 of CPR (Regulation (EU) 2021/1060), Member States can transfer up to 5% of their ERDF allocation to HE to support excellent but unfunded proposals from their region. The process requires approval from the Monitoring Committee (MC) and justification that the transfer benefits the transferring region. Once approved, the funds are used in the following calendar year under HE rules.

Cumulative funding

Cumulative funding allows a synergy project to receive support from multiple EU funds (for example, HE and ERDF) for the same eligible costs, up to 100% of funding from the EU budget, provided it complies with State aid rules. It’s a great opportunity to spread the financial burden of an operation and to address possible budgetary constraints on the side of a Member state.

European Partnerships

European Partnerships address EU priorities by pooling public and private resources, coordinating R&I investments, and strengthening cross-border cooperation, while enabling ERDF contributions as national inputs to boost participation from less developed regions and align with HE and S3 priorities. They drive synergies by integrating national research programmes, enhancing complementarities, and ensuring that underrepresented Member States can engage in transnational collaboration.

There are two types:

• Co-funded Partnerships: Consortia of national funders receive HE co-funding (usually 30%), with ERDF covering part of the national contribution.
• Institutionalised Partnerships: Long-term initiatives under Articles 185 or 187 TFEU (e.g., Joint Undertakings), where ERDF can contribute as a national input.

Combined funding (Teaming)

Teaming action supports the creation or modernisation of centres of excellence by connection with a leading research institution from a different country. To make it happen, complementary funding (from national, regional, EU, or private sources) is often required, for which the compatibility conditions to grant State aid (including from ERDF resources) are outlined in Article 25d of Commission Regulation (EU) No 651/2014. Teaming is seen as a way to bridge gaps between regional strategies (like Smart Specialisation Strategies) and top-level research, strengthening Europe’s overall research and innovation landscape.

Upstream and downstream synergies

Upstream synergies involve using Cohesion Policy funds to strengthen R&I capacities, enabling better participation in Horizon Europe. Downstream synergies, on the other hand, use CP funds to scale up and adopt the results of HE projects at national and regional levels.

When HE and CP funds are coordinated effectively across all stages of innovation – especially in line with EU priorities – they can amplify the impact of innovations and deliver wider social and economic benefits across the EU. Achieving these synergies depends on close collaboration between key stakeholders, particularly the EU and national authorities responsible for programming and implementing Horizon Europe and Cohesion Policy funds.

Lessons Learned and Current Outlook

Despite progress since the 2014-2020 period, the adoption of synergies between Horizon Europe and Cohesion Policy funds remains slow in 2021-2027, concludes the 2025 Report “Exploring Synergies between Horizon Europe and the EU Cohesion Policy”, provided by the Policy Department for Transformation, Innovation and Health (DG ECTI) at the request of the European Parliament's Committee on Industry, Research and Energy (ITRE).

According to the Report, overall, the implementation of synergy mechanisms varies. The Seal of Excellence schemes are expanding, and ERDF-to-HE transfers have succeeded in Malta and Lithuania, but challenges like funding constraints, administrative duplication, complex coordination, and regulatory misalignments hinder broader uptake. At the same time, downstream synergies, in particular, remain underutilised, though initiatives like the Pathway to Synergies HE call aim to address this.

To unlock the potential of synergies in question, the Report recommends that policymakers should simplify regulations, harmonise frameworks, and strengthen coordination (e.g., via the RIMA network). Targeted capacity-building, clearer guidance, and better data collection would reduce burdens, align priorities, and help stakeholders leverage synergies for greater innovation and economic impact. And these recommendations are getting addressed.

As of 2026, the EU continues to emphasize the importance of synergies between Horizon Europe and Cohesion Policy funds to bridge the innovation divide, particularly for widening countries. The 2026-2027 Horizon Europe Work Programme expands the implemented instruments with Teaming Synergies and the Research Management Facility, specifically designed to foster collaboration, sustainability, and capacity-building in less advanced regions. These efforts aim to ensure that research and innovation benefits are shared more widely, aligning with the EU’s goals of reducing regional disparities and strengthening the European Research Area.

For Ukraine, which has been associated with Horizon Europe since 2022 and has an HE office since 2023, these synergies offer valuable lessons. The EU’s experience with synergies highlights the need for regulatory simplification, strategic alignment, and capacity building - lessons that Ukraine can adopt to maximize the impact of EU funding and foster a resilient, innovative future. By leveraging these mechanisms, Ukraine can accelerate its recovery, deepen its integration into the European research and innovation landscape, and ensure that its regions - each with unique strengths and challenges - can benefit from the regional policy complemented by innovation ecosystems built on local talent but national and international opportunities.