In April 2006 alongside Chantal Groot, Hinkelien Schreuder and Inge Dekker, Veldhuis set a world record and won the gold medal in the 4×100 m freestyle relay at the 2006 FINA Short Course World Championships. She failed to defend her 50 m freestyle title ending third. She finished second behind long-time rival Libby Lenton in the 100 m freestyle. In the summer she competed in the 2006 European Aquatics Championships, in Budapest, Hungary where she ended second in the 100 m freestyle, behind German's Britta Steffen who broke the world record, and third in the 50 m freestyle. In the 4×100 m freestyle relay she received a silver medal together with Chantal Groot, Inge Dekker and newcomer Ranomi Kromowidjojo. After these Championships she split up with her coach, Fedor Hes, and started to work with Jacco Verhaeren, who at the time was also working with triple Olympic champion Pieter van den Hoogenband. In Helsinki she successfully defended her 50 m and 100 m freestyle titles at the European Short Course Swimming Championships 2006, but lost her relay titles when her team ended second in the 4×50 m freestyle and did not start in the 4×50 m medley. Just before this championships she had bettered Annemarie Verstappen's long standing 200 m freestyle national record.