Abstract Background The EU-funded Marie Curie project HEALTHPROS aims to foster a new generation of “Healthcare Performance Intelligence Professionals” through a cohesive stream of 13 doctoral projects (www.healthpros-h2020.eu). Over 48 months, researchers will investigate key levers of healthcare improvement in 7 different countries, using methods drawn from the diverse fields of biostatistics, medical informatics and health services research. Objectives To describe barriers and enablers in the conduction of two doctoral projects aimed at exploring the impact of personal risk factors and organizational arrangements on lower extremity amputations in diabetes, through the use of large-scale databases from England, Scotland, Denmark and Germany. Results The research plan included a systematic review, structured comparison of data sources, predictive modelling and software development for automated international comparisons. Barriers encountered by researchers were: knowledge and access to data sources from different countries, dealing with data protection rules and the ability to carry out international comparisons when individual records are not easily allowed to leave national boundaries. Enabling factors included: a targeted educational process for risk modelling in diabetes and a multidisciplinary support team to help doctoral students overcoming the above barriers across different sites. Further clinical insight and contextual knowledge of data systems in place at different locations were needed in addition to the statistical, epidemiological and technical skills initially foreseen by the program. Conclusions The success of studies within a general educational program on health systems performance may depend from the continued support of a multidisciplinary team helping students in their educational process as well as with the practicalities of their research. International comparisons using routine data may require prioritisation to meet the tight timelines of doctoral theses. Key messages Academic programs for international comparisons in health care may be hampered by different type of barriers including technical aspects, legal regulations and a range of contextual factors. The establishment of multidisciplinary support teams may be essential for training doctoral students aiming to conduct international comparisons using routine data.