Background: In today’s world, where life-science research is becoming increasingly data-driven, unequal access to formal bioinformatics training constitutes a significant limitation for the effective use of insights derived from continuously generated biological big data. This gap is especially pronounced in low- and middle-income countries, including the Central and Eastern Europe (CEE) regions, often struggling with insufficient computing infrastructure, training facilities, and local expertise. To address this issue, we present a comprehensive framework to boost regional development of bioinformatics capacity through intensive, targeted short-term workshops in a hybrid format, which maximize accessibility, while fostering international collaboration and knowledge exchange among participants. We describe our experience with model’s implementation on the example of the East European Bioinformatics and Computational Genomics (EEBG) workshop series - a cross-disciplinary initiative rotating between host institutions in CEE to deliver cutting-edge knowledge in the way that takes into account regional educational peculiarities and needs. Analysis of the 2025 EEBG edition in Kraków, Poland (42 on-site, 70 remote participants) demonstrates high satisfaction with practical skill transfer and networking opportunities, while also highlighting challenges common for hybrid education, such as the reliability of audio/visual equipment and the appropriate pacing for groups with mixed levels of experience. Based on those observations, we identify refinements and outline core design principles for effective, scalable bioinformatics training.