Wotquenne was born in Lobbes, Hainault, Belgium. He studied at Brussels' Conservatoire Royal, where his teachers included Louis Brassin (piano), Alphonse Mailly (organ), and François-Auguste Gevaert (theory). In 1894 he was appointed the chief librarian of the conservatoire; he retained this post until 1918. During his time the library acquired a great many works, both printed and in manuscript.
The best known of Wotquenne's achievements is his 1905 bibliographical study of C.P.E. Bach, but he also performed similar services for other composers: Baldassare Galuppi (1900), Christoph Willibald Gluck (1905), and Luigi Rossi (1909). He also contributed to a complete inventory of the works of a fellow-Belgian, the Liège-born André Grétry.
Thanks to Wotquenne's efforts, C.P.E. Bach's pieces came to be known by their Wq numbers. They are now also known by their H numbers, from a new and more thorough catalogue by Eugene Helm (1989). A concordance between these systems is available.
By royal decree he lost the Order of Leopold, and his position on 9.8.1919, he was convicted for participating with the enemy. He was arrested in 1918.
From 1921 Wotquenne lived in France, working in Antibes as a choir master and organ teacher. He died at Antibes shortly after the outbreak of World War II.
- Catalogue thématique des œuvres de Chr. W. v. Gluck. Breitkopf & Härtel, Leipzig 1904
- Catalogue thématique des œuvres de Charles Philippe Emmanuel Bach (1714-1788). Breitkopf & Härtel, Leipzig 1905
- Grove's Dictionary of Music and Musicians, 5th ed, 1954, Vol. IX, p. 368
- Indexes, Concordances, and Other Material for the Study of Music by C.P.E. Bach
- KB 9.8.1919: Leopoldsorde Schrapping: Werkdadige hulp aan den Vijand