Don Henley has described "The Heart of the Matter" as the toughest song of his career, one that took him decades of lived experience to be able to write, even though he had already co-written hits for the Eagles such as "Hotel California" and "The Long Run". The song, completed in 1989 for his third solo album, The End of the Innocence, only came together after Henley endured a painful break-up and reached a level of emotional maturity he didn't possess in his younger years, making it a deeply personal piece rather than a calculated bid for radio success.

Henley co-wrote the track with JD Souther, who had also recently split from his fiancée, and the pair drew directly on their shared heartbreak. Souther told SongFacts that, despite the raw subject matter, the writing process itself was straightforward, and that the song's theme of forgiveness benefiting the person who forgives was Henley's idea. Rather than channelling anger towards their former partners, the two chose a compassionate approach that Souther said gave the song a universal resonance, something Henley felt he could not have written with the same honesty five or ten years earlier.