In his research Jan Bouwens focuses on the question of how accounting affects collaboration among business units. He is examining whether and, if so, under what conditions the use of profit numbers at the business unit level prevents managers from taking account of the interests of fellow managers who are in charge of other business units. Another aspect of his research is focused on whether accounting standards, such as profit and customer satisfaction, induces managers to pursue short-term results. With this study Bouwens tries to provide some preliminary answers to the question of whether performance-related remuneration induces managers to put the existence of the company at risk by over-emphasising the short term. In the next few years Bouwens plans to focus on two main themes: accounting and the structure of relations that reside inside a company, and the role of cost information in making decisions. With regard to the structure of relations, he plans to examine whether the use of accounting over time influences mutual trust. A study he conducted at a major transportation company revealed that managers cooperate better with each other if they regularly meet in the flesh. In his cost study Bouwens aims to focus on whether the use of sophisticated cost information minimises the risk of enterprises being besieged with innovations which jeopardise their continued existence.

Until 1 September 2015 Bouwens was professor of Accounting at Tilburg University. From July 2013 to July 2014 he held the post of visiting professor of Accounting in the MBA programme at Harvard Business School. He also is a research fellow at the University of Melbourne in Australia.

Bouwens has published articles in numerous leading scientific journals in the field of accounting, including the Journal of Accounting and Economics, the Journal of Accounting Research and The Accounting Review. He is associate editor of the Journal of Management Accounting Research and the Journal of Contemporary Accounting & Economics. He also is a member of the editorial staff of Contemporary Accounting Research and of the Dutch accounting journal MCA, which he headed from 2004 until 2010. Bouwens was also in charge of the PhD programme in Accounting at the interuniversity Limperg Institute and is a founder of the Accountancylab, a new research institution funded by the Dutch audit offices.

Bouwens has written policy reports for the Ministry of Finance and the Dutch parliament relating to the work of an accountant and the organisation of supervision. Dutch newspapers regular publish his opinions. He writes editorials for De Accountant.

He lectures in management accounting and control mainly in graduate and executive programmes. Bouwens is also regularly invited to provide PhD training programmes by internationally renowned universities. He has held seminars at universities including Cambridge, Chicago, and Harvard, as well as at the London School of Economics and Political Science. At the UvA Amsterdam Business School, he will be in charge of the Registered Accountant (PMA) and Registered Controller post-Master's programmes (EMFC).