Lyndsay's main research interests include gender, gender violence, conflict and violence, ethnicity, reconciliation and social transformation. Her PHD research focused on the relationship between ethnicity, violence and reconciliation in Rwanda. She looked at how the categories "Hutu" and "Tutsi" were understood, used and experienced in the everyday lives of young Rwandans living in Rwanda a decade after the 1994 genocide and young people's perspectives on the reconciliation process.

Lyndsay has also conducted recent research on violence against women for UNWomen, looking at the nature and prevalence of various forms of violence East Timor and how and why such violence persists. She also managed similar research in Uganda, Liberia and Haiti based on the same methodology. She is part of the DFID-funded Research and Innovation Fund 'What Works to Prevent Violence Against Women and Girls' and is co-PI for a reserach study on the impact of a GBV prevention intervention in Rwanda, as well as advising other projects.