The ordeal is not yet over for emergency crews and residents.
"I was coughing, coughing, and trying to get my breath, and I'm still kind of having a little aspiration from it," said Beverly Browne who lives nearby.
The fire broke out Saturday with flames reaching into the sky. The Santa Clara County Sheriff's Department helicopter captured video and residents came from all over to take their own.
"I wanted to see how it looks right now in person," said resident, Tina Talmoud.
"I'm just like how does that happen because all buildings are supposed to have sprinklers," said Maureen Burt of San Jose.
San Jose firefighters said the blaze may have started in the lumber and drywall section of the store.
Fire protection experts said these types of big box stores present particular challenges: that there will be certain sprinkler systems designed to handle lumber fires and others for chemicals.
"If paint cans or heavy plastics start making their way there, that's going to start compromising your fire protection system, your sprinkler system," said Brian O'Connor with the National Fire Protection Association.
The Bureau of Alcohol, Tobacco, Firearms and Explosives agency was on the scene Monday to begin its investigation along with dozens of restoration crews ready to begin the clean-up effort.
"This is about a $6 million fire loss," said Junior Guadalupe Salinas with Giuliani Construction and Restoration.
The company hopes to submit a bid for work.
They said this will be a giant project and a sensitive one given the nature of the fertilizer, paint, and other materials inside.
"We're out here of course looking at the fire and seeing what we can do as far as assisting for services," said Salinas.
The San Jose Fire Department released a statement today saying they're working to put out flare-ups from debris trapped below the collapsed roof. The department is still working to determine a cause.