Some weeks later, Remus began working as a spy for the Order, living among fellow werewolves and trying to convince them to join Dumbledore's side. It is said that he volunteered just to keep away from Tonks, as they were both very much in love with each other by this point and he would not risk his child having lycanthropy. Alas, it was difficult to convince them due to the fact that they believed they will have a better life under Voldemort's reign, many were frightened and intimidated by Fenrir Greyback and that Remus showed signs of living among humans.

Weeks later, on Harry's 16th birthday, Remus visited The Burrow with news of Dementor attacks and murder of Igor Karkaroff.

During Christmas at the Burrow Harry told Remus and Arthur Weasley about the overheard converstion between Draco Malfoy and Severus Snape. Mr Weasley immediately suggested that Snape was just pretending to help Malfoy, but Lupin severely pointed out that Dumbledore trusted Snape, which "ought to be good enough for all of them.” Although Snape exposed Lupin as a werewolf, forcing him to resign his position at Hogwarts, he also kept him healthy by making him a special potion during his monthly transformation. Lupin neither liked nor disliked Snape – but personal feelings have nothing to do with his decision to trust him. Lupin argued strongly against making judgments based on feelings – even though he, of all people, had strong reasons to dislike Snape personally, he refused to let this affect his conclusions about the man. This pronouncement established him as a foil to James Potter and Sirius, who disliked Snape for petty reasons and treated these feelings as a justification for bullying him.