Menlo Park Fire Protection District Division Chief Fire Marshal Jon Johnston said they think the fire started on the fifth floor but it's still unclear how.
Despite there being 130 workers on site, nobody was hurt and fire officials say dozens of construction workers evacuated safely.
PREVIOUS: Evacuation orders lifted for residents impacted by 8-alarm affordable housing fire in Redwood City
"We have one of two buildings that were under construction," Division Chief Johnston said. "The one that burnt was a [104-unit] apartment complex that was in the process of being sheet-rocked and insulated, in the phase of construction."
This was a $155 million affordable housing project a decade in the making. It was slated to have 179 units in all, a childcare center and more. It was a joint effort by San Mateo County and Mercy Housing.
In a statement to ABC7 News, the contractor James E. Roberts-Obayashi Corp. said that this was the worst disaster in its 92-year history.
MORE: Multiple structures burn in East San Jose fires; no injuries reported, SJFD says
One-hundred homes were evacuated Monday. The building is now considered a total loss.
Strong wind not only made it a difficult firefight, it also led to spot fires and debris that spread across a wide radius.
"We had debris all the way down into Palo Alto I'm hearing this morning which is amazing," said Jon Johnston, Division Chief Fire Marshal with the Menlo Park Fire Protection District.
Still that fire was most dangerous for those who lived right next to it.
"When I evacuated the flames were already over (the house) and the heat was so intense and embers falling I was for sure like 'We're gonna lose the house'", James Smith Said.
James and Michelle Smith were finally able to go back into their home Tuesday morning after an overnight evacuation.
Michelle said that they moved fast to protect their home when the fire first broke out Monday.
"He ran out with the water hose, and he started just basically watering our backyard and our neighbor's yards," she said.
Their house was spared though their backyard is torn apart, the downed fence revealed more of the extensive damage done to the building.
The Menlo Park Fire Protection District said Tuesday that the cause was still under investigation.
The affordable housing project was planned to have 179 units.
It was a joint effort by San Mateo County and Mercy Housing.
Fire crews continued to monitor hotspots more than 24 hours after the fire was contained and said they'd stay in place for as long as needed.