The PlantaSYST project aims at establishing a new Plant System Biology and Biotechnology Centre (CSCBB) in Plovdiv, Bulgaria. The CRCB is registered as an independent legal entity whose main activity is research. The CRCBB is supported by the Bulgarian and German partners under the PlantaSYST project, the governments of both countries and the Municipality of Plovdiv. The mission of the CRCB is to have a leading position in the field of plant sciences in Europe. Advanced techniques in functional genomics, metabolomy and bioinformatics will be used to identify regulatory mechanisms and metabolic pathways that govern plant development, stress physiology and the synthesis of potential valuable metabolites to find market applications. The fundamental research carried out in the Departments of Plant Development, Physiology and Molecular Bases of Stress, Metabolomy and Bioinformatics will be included in the applied research of the Plant Cell Biotechnology and Vegetable Crop Production Departments. The CRCBB will be a link between academia and industry in the region and will lead the training of a new generation of researchers in the field of plant system biology and biotechnology. In this way, CRCBB will meet the criteria set out in the Innovation Strategy for Smart Specialisation of the Republic of Bulgaria 2014-2020 (Biotechnology). The technology transfer office will support the flow of knowledge and technology to partners and end users. In conclusion, the newly established Centre of Excellence CRCBB will significantly increase Bulgaria’s research potential, expand the country’s capacity in the field of plant genomics and stimulate the development of the scientific and economic potential of Plovdiv and the region. The funds of the present procedure provide for the construction of a new campus of CRCBB and a building equipped with modern equipment.