Fraser cited her move to Los Angeles as a major inspiration, saying "I was really frustrated and felt like I needed to get away and be somewhere where I could completely focus...and just to try and get a little bit of head space. It was the best decision we ever made". She called Flags "a graduation". Writers of tracks on Flags include Fraser, her husband Scott Ligertwood, and Switchfoot's Jon Foreman. The album was produced by Fraser herself. According to Fraser, "Crows + Locusts" was inspired by a farming family, while "Ice on Her Lashes" is about death and grief. "Betty" is based on hiding things. The title track, "Flags", was brought about by cultural identity and injustice.