The album has received generally favorable reviews in the years since its initial release. AllMusic's Johnny Loftus said that Against the Grain "found the band's edge honed sharper than it had been in years", and claimed that "Bad Religion had always warned against the excesses of the future and the assimilation of individuality. But the gospel cut deeper with Against the Grain. Songs began in an instant, with the single crack of a snare drum signaling the beginning of another screed."
