Public procurement for innovation is a tool for the legal arrangement between the state - which demands technical solutions to problems, new products, services, or processes - and the company or institution that can develop and manufacture them. The objective of this paper is to analyze the variables, risks, and uncertainties that affect procurement for innovation in the software sector, based on experiences with this legal tool in the state of São Paulo. The research was descriptive and had as its axis of analysis the flow of public procurement, from its design, through implementation and control. From the analyzed experiences, we sought to outline possible measures and strategies to be adopted by contract managers to deal with the categories of risks and legal-institutional uncertainties identified.