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Main objective of the study is to analyse the impact of portfolio management on the level of quality in EU projects implemented in public universities. First part of the article is theoretical and prepared on the basis of a critical analysis of literature in the field of quality management in projects and project portfolios. Second part of the text was based on primary data collected during preliminary survey conducted among EU project managers implemented in public technical colleges in the 2014-2020 financial perspective. Literature studies and results of own research allowed to identify and assess threats affecting the quality level in EU projects that result from transition from the level of individual project management to the level of project portfolio management. Continuous improvement of quality is a characteristic feature of organizations using quality management systems, so the article indicates the need to have an internal quality assurance system at universities. Importance of organizational units managing EU projects in universities in ensuring that products and results of a project are of high quality have also been underlined.