MacGregor made her conducting debut in 2002 and regularly directs her own orchestral projects, including an all-Mozart programme with the Royal Philharmonic Orchestra and Bach with the Hallé. She enjoys a close artistic partnership as conductor and performer with Britten Sinfonia, in programmes ranging from classical music to collaborations with jazz and world musicians, including Andy Sheppard, Seb Rochford, Nitin Sawhney and Arve Henriksen. In 2009 she opened the London Jazz Festival with Britten Sinfonia and Arabic singer and oud virtuoso Dhafer Youssef, hailed by "The Times" as 'the future of music'. Their fifteen-year orchestral partnership has continued with tours in Europe and Latin America.