The assessment of university-industry collaborative projects has been complex and has become more prevalent in national research, educational and innovation system reviews. One criticism made about studies of university-industry collaboration (UIC) is they are too much orientated towards exclusively the outputs (Rossi and Rosli in Stud High Educ 40(10):1970–1991, 2015) and that there is a need to apply case specific metrics. To address this criticism we have taken Brown et al’s Res Technol Manag 31(4):11–15, (1988) R&D lifecycle of inputs, in-process activities, outputs and impact at micro level to examine what are the common and context specific key performance indicators of UIC. Taking a qualitative approach and using university-industry collaborative projects set in Finland and Russia our study identified a common set of micro level KPIs across the UIC lifecycle at a micro level. Namely, the amount of resources allocated by partners to collaboration; efficiency of collaboration management and clearly defined roles; as well as a number of company innovations resulting from collaboration with a university and new strategic partnerships. Our study also found contextual micro level KPIs as number of young researchers involved, fit between collaboration and organizational strategy; number of joint publications; enterprise image improvements. Our research extends the existing knowledge on UIC KPIs in the following ways. First, we define those KPIs, which are applicable by all the three actors of the triple helix, but also identify those that are not used by some of these actors. Second, we analyse the relevance of certain KPIs proposed by governmental bodies and the literature in terms of their applicability in the analysed case studies. Finally, we define those metrics, which among other existing KPIs depend on the case context (region, research area, industrial sector and partners’ goals) as well as identify additional KPIs, which have not received attention in UIC literature.