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 four-large RCTs on improving literacy levels for students in schools. His pedagogic 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 Board of Technology, Pedagogy and Education, Pakistan Journal of Special educational Needs, 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, and is currently Chair of the SIG awards committee. 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 the Academy of Globalization and Education Policy, Zhengzhou University, China and a Visiting Professor at Laboratorio de Economia de la Educacion, Pontifica Universidad Javeriana, Colombia. Allen is a member of the REF2021 Unit of Assessment Panel for Education.

Allen is a member of The Commonwealth Scholarship Commission Academic Adviser Panel. He is also a mentor for the Council for At Risk Academics helping mentor academics who have been displaced by war or persecution. He is currently working with a group of Syrian academics who have country of safety status in Turkey. He is a Governor for a local cross-commity post-primary school. He has been an active member of mountain rescue teams in Scotland and Northern Ireland for over 30 years. He is currently the call-out office for North West Mountain Rescue Team, initiating call-outs when requested by PSNI/Garda.