In a follow-up ESPRIT-II project Kersten was responsible for the development of an enhanced version of SQL for documents and geographical data.

At the same time he started the ESPRIT-III Pythagoras project aimed at performance quality assessment of advanced database systems.

[3] Kersten was an active reviewer for European Strategic Program on Research in Information Technology (ESPRIT) projects and scientific publications.

Moreover, he was a trustee of the VLDB Endowment board, which aims to promote and exchange scholarly work in databases and related fields worldwide.

[9][10][11] In August of the same year, Peter Boncz, Stefan Manegold and Martin Kersten received the VLDB 10-year Best Paper Award for their publication titled "Database Architecture Optimized for the New Bottleneck: Memory Access".

MonetDB (initially only called Monet) was first created by 2002 doctoral student Peter Boncz and professor Martin Kersten as part of the 1990s MAGNUM research project at University of Amsterdam.

MonetDB also features automatic and self-tuning indexes, run-time query optimization, and a modular software architecture.

[35][36] In 2013 Martin Kersten, together with Ying Zhang, Niels Nes and Sjoerd Mullender established a database services CWI spin-off company.