Winninghoff studied classical trumpet with Huug Steketee and jazz trumpet and flugelhorn with Ack van Rooyen at the Koninklijk Conservatorium Den Haag from 1991 to 1993. He continued his studies until 1998 at the Musikhochschule Köln with John Marshall and Markus Stockhausen. He also participated in workshops with Kenny Wheeler, Bill Evans, Peter Erskine, Gary Peacock and Bob Brookmeyer. As a member of the Bundesjazzorchester under Peter Herbolzheimer, he toured Romania, Moldova, Ukraine and South Africa.

In 1995 he won the nationwide jazz young talent competition in Leipzig with the Christian Winninghoff Group, with whom he recorded his first album as a bandleader in 1998. Between 2000 and 2003 he performed in duo concerts with pianist Jürgen Friedrich. Since 2000 he has been a member of the group Jazzkantine and participated in several of their albums as a performer and arranger.

He has also worked with the Niels Klein/Calle Rasmussen Jazz Quartet, the Oktoposse Jazz Oktett and the ensembles of Ulla Oster, Matthias Petzold, Klaus Fey, Caroline Thon, Gabriel Pérez, Hinrich Franck, Maxime Bender and Rainer Tempel. Crossing genres, he has worked with Markus Stockhausen, Terry Bozzio and Michael Riessler. As a studio musician he was active for Heinz-Rudolf Kunze, Jean Shy, Marla Glen or the Heavytones.

From 1998 to 2000 Winninghoff taught trumpet at the Musikhochschule Köln, since then he has been a lecturer at the Städtische Musikschule Langenfeld. He has published several textbooks.