Allen's research interests include improving learning in schools and research methods. His school based work looks at how to raise attainment for those students from socio-economic disadvantaged backgrounds. He predominantly uses randomized controlled trials (RCTs) and is currently running two-large RCTs on improving literacy levels for students in schools. His pedagogicl expertise lies in the area of cooperative/peer learning. He has published extensively in this area.

Allen is Editor in Chief of International Journal of Educational Research (IJER). He is on the Editorial Boarda of Technology, Pedagogy and Education, and Educational Psychology. He was awarded the 2013 American Educational Research Association (AERA) Cooperative Learning SIG award for 'Outstanding Research Contribution in the Field of Cooperative Learning'. He served as Secretary/Treasurer of the AERA Cooperative Learning SIG from April 2014 until April 2017. He is a member of the ESRC Peer Review College and has Reviewed Grant Applications for Social Science Research Councils in Canada, Portugal, Oman and the Netherlands. Allen is a Distinguished Visiting Professor at Zhengzhou University, China.