The use of biowaste as a resource allows for the execution of the EU common objectives regarding the minimization of the deposited amount of biodegradable waste. Also, by using biowaste to convert waste to energy (biogas, waste incineration) the reuse of waste materials increases. Unfortunately, organic waste management is underdeveloped in the Baltic States. The aim of this research is to find an optimal solution for biowaste treatment for the conditions in the Baltic States. Furthermore, the assessment of different scenarios through a multi-criteria sustainability assessment will occur. This paper discusses the application of biowaste management systems for energy issues in the region by integrating ecological, socio-economic and economic aspects. This paper presents an analysis of the possibilities to utilize biowaste for energy production in the Baltic States, including biogas production from landfill gas and biogas production from biowaste by the method of anaerobic digestion and waste incineration.