From 2004 -2011 he was Chief Scientific Officer of Crucell and member of the Management Board. When Crucell was acquired by Johnson and Johnson Goudsmit became head of the Crucell Vaccine Institute from 2011-2015, an institute focusing on influenza research.
Between 2004 and 2011, he served as Chief Scientific Officer at Crucell and sat on the Management Board. Following Crucell's acquisition by Johnson and Johnson in 2011, Goudsmit took over as head of the Crucell Vaccine Institute until 2015, a research center specializing in influenza studies.