Deputies went to the restaurant at 40 Stone Pine Road at 6:15 p.m. and arrested 27-year-old Pedro Jeronimogonzalez, a part-time employee who had been working at the restaurant for about six months.
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"Everybody here is kinda in shock, but I think we just can't believe this could happen to our customers -- that's the part that really hurts," said Jersey Joe's Coastside owner Don Godshall.
The business is known as a family place where kids go after soccer practice, according to Godshall.
Police were called as soon as the discovery of the phone was made, he said.
Sheriff's officials allege that the cellphone was placed in the restroom intentionally and belonged to Jeronimogonzalez.
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Investigators allege the cellphone captured six people, two women, and four children, on video. No other details about the case are being released yet, according to the sheriff's office.
Jeronimogonzalez was taken to the county jail. The allegations against him include disorderly conduct, child exploitation, and wiretapping, according to the sheriff's office.
Officials say two women and four children were recorded and they need to identify those victims.
"Your privacy and your dignity is very important to us but right now what we want to do is hold the suspect accountable for his actions," said Detective Salvador Zuno of the San Mateo County Sheriff's Office.
Detectives are asking customers who visited Jersey Joe's Coastside on Saturday between 5:30 p.m. and 6:15 p.m. to get in touch with them. Anyone with information about the case is being asked to contact Detective Pat Carey at (650) 259-2321.
Information can also be left anonymously on the sheriff's tip line at (800) 547-2700.
ABC7 News' Katie Marzullo contributed to this report.