Miranda, who went from being a broke substitute teacher to creating "Hamilton," tells NBC's Today that, like many other Americans, he has family on the island he could not communicate with after the hurricane.
"What we all experienced, if we weren't from the island, was this terrible silence in the wake of the storm," Miranda says. "Our social media feeds were full of the names of towns," where people had still not heard from their families.
Inspired by this, Miranda incorporated Puerto Rico's 78 towns into the lyrics of the songs.
He also included 21 musical features, many who were Puerto Rican, including singer Luis Fonsi (of recent "Despacito" fame) and Forbes Celebrity 100's millionaire Jennifer Lopez.
"Almost Like Praying" lifts its hook from a line in the song "Maria," featured in Broadway show "West Side Story," according to the Associated Press. Miranda said the song came to mind after the hurricane by the same name devastated the island.
"I knew that name would forever have a destructive connotation on the island and yet I have a musical theater brain, so that's where I went in my head first," Miranda tells Today.
"Thoughts and prayers are great. Thoughts and prayers are not enough," Miranda tells Today. "We need supplies, we need aid, we need a government response that matches the response of our people. That's what this song is about."
Thanks to "Hamilton," Manuel has earned 11 Tony Awards, a Pulitzer Prize, a Grammy Award and at least $6.4 million.
Earlier this week, Miranda helped "Late Show" host Stephen Colbert raise $1 million for his Puerto Rico hurricane relief efforts.
Like this story? Like CNBC Make It on Facebook.
4 questions to ask yourself to figure out what you really want in life
Warren Buffett says this one investment 'supersedes all others'