Public-Private Partnership (PPP) is one of the most innovative procurement methods for an infrastructure project that is currently in high demand in Indonesia. While this scheme offers many advantages, the most significant benefit is a more proper risk allocation between the public and private sector. The risk-sharing between the two parties could be implemented in the whole project cycle, including when the project should decide its funding resources, which could be directly from the end-user (User Charge), or the annual government payment (Availability Payment). Despite the importance of risk and funding method, this study found only a few previous works of literature that are focussing on how risk could affect the selection of PPP project funding mechanism. Therefore, this research aims to identify the risks and the stakeholder preference for PPP funding mechanism in the Indonesian context. This study performs semi-structured interviews as a qualitative data collection method. The interview participants are from numbers of PPP practitioners in Indonesia with various professional backgrounds. After several series of interview, this study found numerous risks that should be considered in the funding selection process that could be categorised into four major risk groups, which are: demand, political, relationship, and financial dimensions. This research also found that the stakeholder preference on the funding selection is classified into three contexts, which are: (1) The types of infrastructure project, (2) Sector maturity, and (3) The degree of risk uncertainty. Additionally, this research then concluded by providing four key-suggestions for a more proper PPP funding selection decision-making, that are: (1) Ensure PPP is the best option in the first place, (2) Make a standardised, integrated, and sustain policy, (3) More balance risk allocation, and (4) Enhance the PPP knowledge in various sectors.