Brüggen introduced a flexibility of tone and rhythm to solo recorder playing that was novel to historically informed performance practice at the time. Notes in slow passages would be slightly bent for emotional affect, tone warmed and cooled, messa di voce employed, alongside considerable use of rubato.[3] Such approaches provoked some controversy at the time, but in part due to his use of them, have since become more commonplace.
In 1981, Brüggen co-founded with Sieuwert Verster the Orchestra of the Eighteenth Century (Orkest van de Achttiende Eeuw).[5] Although he did not have a formal title with the orchestra, he was its de facto chief conductor until his death.[2] The Orchestra of the Age of Enlightenment (OAE) named Brüggen its co-principal guest conductor, in parallel with Simon Rattle, in 1992. The OAE later gave him the title of Emeritus Conductor in 2007. He was the conductor of the Radio Kamerorkest in the Netherlands from 1991 to 1994, and joint chief conductor of the orchestra, alongside Péter Eötvös, from 2001 until the dissolution of the orchestra in 2005. Brüggen conducted the final concert of the successor to the Radio Kamerorkest, the Netherlands Radio Chamber Orchestra, on 14 July 2013.
Brüggen was married twice. His first marriage to Ineke Verwayen produced two daughters, Laura and Alicia.[9] His second marriage was to the art historian Machtelt Israëls, and produced two daughters, Zephyr and Eos.[10] Brüggen was the uncle of recorder soloist and Amsterdam Loeki Stardust Quartet member, Daniël Brüggen.