Material flow management has become an increasingly important paradigm in waste management. An essential goal of this paradigm is prioritizing waste reduction over reuse and recycling, and the latter waste management processes over secure disposal of waste residues. Separate treatment of biodegradable waste fractions (bio-waste) is a promising way to approach this goal. However, compared to Switzerland, many countries only treat a small proportion of their potentially recoverable bio-waste separately. To identify the parameters (impact factors) and mechanisms involved in successful material flow management favoring separate bio-waste treatment, we analyzed the past developments of bio-waste delivery to centralized transformation facilities in Canton Zurich, Switzerland. In so doing we performed (i) an agent oriented material flow analysis; (ii) a structured selection of relevant impact factors influencing the material flow development; (iii) expert interviews to assess the adequacy of the set of impact factors and their mutual interactions; and (iv) a cross impact analysis to reveal the relevance of the impact factors and their interferences that make up regulatory mechanisms. Our analysis shows that complex interactions of various impact factors lead to the particular material flow developments of the Zurich bio-waste supply market. Four important aspects contributing to its success were that: (i) the cantonal agencies created, in cooperation with private stakeholders, a flexible framework encouraging rather than restricting the developments; (ii) a creative and financially powerful innovator made use of this framework; (iii) separate bio-waste transformation was cheaper than incineration; and (iv) the technological and societal boundary conditions were beneficial to the developments.