In the 11th century, the church was busy fighting heretics, and two of its greatest warriors were Leon Belmont (the warrior) and Mathias Cronqvist (the tactician). When monsters appeared, Leon requested to be able to fight them, but the church was more interested in fighting heathens than monsters, and forbid it. When his betrothed was captured, Leon had to renounce his title in order to save her. This began centuries of estrangement between the Church and the Belmont Clan.
In the 15th century, the Church employed Sypha Belnades, a witch, who disguised herself as a priest and a man. She was the church's greatest warrior, and her descendants would continue to serve the church for centuries. When Dracula began destroying the humans, the Church sent an army to Dracula's Castle, and they were annihilated by the armies lead by the devil forgemasters Hector and Isaac. They sent Sypha to deal with Dracula, but she was captured by the Cyclops and turned to stone. With no one else to turn to, they sought one of the outcast Belmonts and found in Trevor a mighty warrior who was up to the task. He rescued Sypha and defeated Dracula. After Dracula was slain, it was found that Dracula's curse still remained. It is not clear if Zead was really working with the authority of the church or not, but he claimed to be a priest who was trying to rid the land of the curse. Zead turned out to really be Death, who was trying to resurrect Dracula using his former henchman Hector. He was forced to use Isaac instead, but Hector defeated both Death and Dracula.
Relationships between the Belmonts and the Church were good after Trevor defeated Dracula. It is not clear if the Belmonts worked as members of the church for the following centuries, but the church did provide them with aid.
After the Belmonts vanished, the Church employed the young Jonathan Morris, the wielder of the Vampire Killer, and Charlotte Aulin, a relative of the Belnades clan with power enough to be seen as a trump card for ultimate victory over Dracula. They sent them to investigate the reappearance of Dracula's Castle during World War II and sent a priest Vincent Dorin to meet and assist them. The two defeated the lord of the castle, a vampire unaffiliated with Dracula named Brauner, and then defeated Death and Dracula after his early resurrection.
The church likely played a key role in the final defeat of Dracula, but was only one of the players in his downfall in 1999. Their employee Yoko Belnades kept close tabs on the Hakuba Shrine which had sealed away Dracula's Castle in an eclipse. Yoko was like an older sister to the priestess of the shrine, Mina Hakuba. Wary of a prophesy that involved the return of Dracula in the year 2035, they sent Yoko to investigate the intentions of the cult founder Graham Jones and sent her to Dracula's castle during an eclipse to prevent him from becoming Dracula. She failed and was stabbed by Graham, but her life was spared by Soma Cruz, a Japanese student who it turned out was actually the true heir to Dracula's power. Soma defeated Graham, but became Dracula; however, he resisted his destiny and defeated Chaos to prevent being consumed by and becoming Dracula.
After Julius Belmont regained his memories, he worked for the Church in conjunction with Yoko. The following year, the Church sent Yoko and Julius to defeat a new cult lead by Celia Fortner from creating a new Dark Lord. Julius used the last of his strength to allow Soma to enter the abyss and ultimately prevent a new Dark Lord from coming into being.