Abstract: This chapter discusses the major challenges in managing a bilateral research and capacity-development program, providing a critical analysis of its achievements. In addition, the planning of the next phase of the Indo-Swiss Collaboration in Biotechnology (ISCB) program is outlined, which offers the advantage of integrating findings and experience from the past. The process for planning and project review under the "new" ISCB is discussed, based on the concept of the "integrated value chain." Finally, the main changes in the organizational setup of the program are reviewed. The chapter concludes with recommendations for international collaborative programs, based on prior experiences, a recent external review of the ISCB, and the current planning process for the new ISCB program.