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.
From 2004 to 2011, he held key roles at Crucell, including Chief Scientific Officer and Management Board member. Following Johnson and Johnson's acquisition of Crucell in 2011, Goudsmit led the Crucell Vaccine Institute from 2011-2015, a research center focused on flu research.