Green transformation at the beginning of the 21st century occupies the top positions in modern society’s sustainability transition research and policy debates due to its multiple propositions of various innovations, addressing the still unsolved issues of rapidly on-going societal and technological changes. Rooting from the general climate change concerns, recently, sustainability transformation has become a special focus in the EU, which is facing new and very concrete demands—to elucidate the evidence-based pathways towards the green transformation with European Green Deal and European Climate Law targets ahead. The main aim of this research is to disclose the pathway towards the green transformation in Lithuania in one of the fast-growing research fields of circular bioeconomy—biogas production from manure and waste. To reach this aim, a hybrid methodology approach was used. Analysis and synthesis of scientific literature, document analysis and structuring, stakeholder mapping, interviews, and statistical analysis methods had been applied. Research results gave evidence for one of the five proposed possible ways for green transformation in Lithuania—the regime transformation. Interviewed stakeholders repeatedly defined this as the most probable pathway for green transformation in Lithuania in the field of biogas production from manure and waste, considering the best suitability of the current development state in the field: adjustments of existing industries, skills, regulations, and institutions.