The overall scope of this study is an attempt at a methodological framework for matching publication lists at the national level against a combined set of blacklists for questionable publishing. Using the total verified set of publications from Swedish Higher Education Institutions (HEI) as a case, we examined the number, distribution, and proportion of publishing in questionable journals at the national level. Journal publication data was extracted from the national SwePub database and matched against three curated blacklists of questionable publishing. For the period 2012–2017, we identified 1,743 published papers in blacklisted journals, equal to an average of 0.5–0.9% of the total publications from Swedish HEIs. There was high variability between different HEI categories, with more established universities at the lower end of the spectrum, while university colleges and new universities had a much higher proportion (∼2%). There was a general decreasing trend during the study period (ρ = 0.83) for all categories of HEI:s. The study presents a methodology to identify questionable publishing in academia which could be applied to other countries with similar infrastructure. Thus, it could serve as a starting point for the development of a general framework for cross-national quantitative estimation of questionable publishing.