Firefighters responded to the blaze around 10:30 p.m. near Colonia Road and Oxnard Boulevard.
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A total of 19 fire engine companies and four ladder trucks tackled the blaze, according to city officials.
It remains unclear how the fire began, but the city described it as "one of the largest fires in Oxnard's recent history."
Crews kept the fire from spreading and spent Wednesday morning extinguishing remaining embers.
"We had extensive ember cast into the neighborhoods, so we had a lot of exposure problems due to the size of the fire," Battalion Chief John Cecena said. "We were able to handle that."
The lemon packing plant has been there since the 1950s back when it was surrounded by lemon groves.
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No injuries were reported, though there is some concern that homeless people may have been taking shelter in the plant. Investigators say they will search inside once the building is deemed safe.
The fire caused four schools to cancel classes Wednesday due to air quality and ash in the area.
Schools will reopen Thursday after an assessment from the Oxnard Fire Department and the Ventura County Air Pollution Control District deemed the area environmentally safe, according to the Oxnard School District said.
A stretch of Oxnard Boulevard and Colonia Road was shut down due to the blaze.