Gospel Music Awards edit
- 1998 Dove Award for Rock Album of the Year for Conspiracy No. 5
- 1998 Dove Award for Rock Recorded Song of the Year for "Alien"
- 1999 Dove Award for Special Event Album of the Year for Exodus
- 2000 Dove Award for Rock Album of the Year for Time
- 2001 Dove Award for Group of the Year
- 2001 Dove Award for Artist of the Year
- 2001 Dove Award for Rock Recorded Song of the Year for "Sky Falls Down"
- 2001 Dove Award for Praise and Worship Album of the Year for Offerings: A Worship Album
- 2001 Dove Award for Special Event Album of the Year for City on a Hill: Songs of Worship and Praise
- 2002 Dove Award for Group of the Year
- 2002 Dove Award for Long Form Music Video of the Year for Third Day Live in Concert - The Offerings Experience
- 2002 Dove Award for Rock Album of the Year for Come Together
- 2002 Dove Award for Rock Recorded Song of the Year for "Come Together"
- 2003 Dove Award for Group of the Year
- 2003 Dove Award for Rock Recorded Song of the Year for "40 Days"
- 2003 Dove Award for Special Event Album of the Year for City on a Hill: Sing Alleluia
- 2004 Dove Award for Praise and Worship Album of the Year for Offerings II: All I Have to Give
- 2004 Dove Award for Long Form Music Video of the Year for Third Day Live in Concert, The Come Together Tour
- 2005 Dove Award for Special Event Album of the Year for The Passion of the Christ: Songs
- 2005 Dove Award for Rock/Contemporary Album of the Year for Wire
- 2006 Dove Award for Pop/Contemporary Recorded Song of the Year for "Cry Out to Jesus"
- 2007 Dove Award for Christmas Album of the Year for Christmas Offerings
- 2009 Dove Award for Pop/Contemporary Album of the Year for Revelation
- 2009 Dove Award for Recorded Packaging of the Year for Revelation