With the advancement of high-throughput, cost-effective sequencing, the application of genomic approaches to biodiversity research is becoming increasingly accessible and inclusive. As the availability of a reference genomes database is indispensable for genomics research, a recent pan-European effort - the European Reference Genome Atlas (ERGA) - was established to scale up the generation of high-quality reference genomes for European eukaryotic biodiversity. Here, we report the results from the GENBUL project, funded by the EU Horizon Europe BGE-ERGA Consortium to support the sampling of reference genomes from biodiversity hotspots in Bulgaria. Focusing on two key biodiversity areas, Slavyanka and Southern Pirin mountains (including the Nature Reserve "Alibotush") and the Strandzha Nature Park, we successfully sampled 190 plant and insect species, including several Bulgarian and Balkan endemics. This effort represents the first major effort for broader-scale genome referencing from Bulgaria and makes an important contribution towards local capacity-building in biodiversity genomics. However, considering the complexity of the genome sampling workflows, standards and metadata management, the GENBUL project also enabled to pinpoint major challenges, currently hindering the deployment of large-scale reference genome sampling in Bulgaria. Based on this experience, we outline key capacity, knowledge and research culture barriers faced by Bulgarian scientists and make recommendations to the international genomics research community for mitigation actions, also applicable to other Southeast European countries.