Numbers for works are cited from: Charles H. Sherman and T. D. Thomas, Johann Michael Haydn. A Chronological Thematic catalogue of His works (New York, 1993.
- 66 Litaniae de Venerabili Sacramento
- 71 Litaniae Lauretanae
- 110 Litaniae de Venerabili Sacramento
- 200/294/304/307 Vesperae pro festo sanctissimae Innocentium
- 215 Lauda Sion
- 532 Litaniae de Venerabili Sacramento
- 654 Hymnus Sub tuum praesidium
Uncertain attributions
- Hob. XXII:G1 Missa pastoralis