Our paper analyzes the development of the current approaches to biodegradable waste (bio-waste) management in the Czech Republic in compliance with the European Union (EU). A proposal for the improvement of bio-waste management following the authors’ long-term research for the Czech Ministry of the Environment has been introduced. The experience of bio-waste management from EU is included in our proposal. The solution to the current situation of the Czech Republic is proposed as a logistically interconnected integrated bio-waste management system of technologies that would optimally manage the specifications of individual groups of biological wastes, the needs of customers, and the possible sale of the final products and/or energies. The proposed solution could also be used by other EU accession countries.