The three were startled by the house's occupant, because they didn't think anyone was in the Spinney Road house when they broke in about 11:30 a.m. Wednesday, police said.
They ran off, but police searching the area found them in a car, questioned them and arrested them, authorities said.
Wilson A. Garcia, 20, and Eli Garcia, 18, both of East Quogue, and Gustavo Gonzalez, 18, of Hampton Bays were arraigned Thursday on two counts of second degree burglary in Southampton Town Justice Court.
Police said they were also responsible for a July 11 daytime burglary at another Spinney Road house. That day, they cased houses on the quiet, residential street and broke into one, taking a rifle, laptop, a PlayStation game, jewelry, coins and a Brinks safe, police said.
Detectives recovered the stolen safe, which they said the three had dumped in a wooded area near Spinney Road.
In Wednesday's burglary, the three men parked their car a few blocks from the targeted house and walked to their break-in, police said.
"They were not deterred by a large German shepherd that resided in the home and brought dog biscuits to distract the animal," police said in a news release. "While inside the home looking for items to steal, the three were startled by an occupant who was still at home, which caused them to flee."
Late Thursday night, Eli Garcia was being held on a $10,000 bail at Suffolk County jail, while Gonzalez was preparing to leave after making his $10,000 bail. It was unclear Thursday night if Wilson Garcia had made his $50,000 bail.