This paper analyses the patterns of Danish research productivity, citation impact and (inter)national collaboration across document types 2000-2012, prior to and after 1) the university mergers in 2006 and 2) the introduction of the Norwegian publication point-based performance indicator 2008/09. Document types analysed are: research articles; conference proceedings papers excluding meeting abstracts; and review articles. The Web of Science citation index (WoS) combined with the Danish Research & Innovation Agency’s basic statistics is used for data collection and analyses. Findings demonstrate that the overall productivity and citation impact steadily increases over the entire period, regardless the university fusions and the introduction of the performance indicator. The collaboration ratio between purely Danish and internationally cooperated research articles remains stable during the period while that of proceedings papers decline. The number of countries with which Denmark collaborate increases for all publication types during recent years in line with citation impact of international cooperation. Simultaneously, the citation impact for conference proceedings papers as such remains substantially the same over the period except for a drop from 2010; their productivity declines slightly since 2009. The ratio between proceedings papers and research articles starts declining from 2009 in WoS corresponding to actual developments observed in the point-based performance indicator itself. Since 2009 the WoS coverage of proceedings papers is declining. The positive growth in research articles derives primarily from the Natural Sciences and Technology published in prestigious Level 2 journals. The introduction of the publication performance model, rather than the university mergers, is regarded the accelerator of these processes in recent years.