Police say the 29-year-old was in the store on Broadway and 71st Street when three men and two women entered around 4:20 a.m.
They pretended to be customers at first before pulling guns and holding up the worker.
They took cash from the register and CBD oil.
When the customer attempted to intervene, one of the suspects shot him in the left foot.
He was taken to St. Luke's Hospital in stable condition.
The customer, from Brooklyn, works at the McDonald's next door was helping out the owner after the same smoke shop was robbed early Friday morning.
In that instance, three suspects entered the store around 6:30 a.m. One displayed a handgun, and the other two hopped the counter.
They stole $40,000 in CBD products and $80 in cash, according to police.
The suspects fled south on Broadway in a light-blue SUV.
Anyone with information in regard to either incident is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
The public can also submit their tips by logging onto the CrimeStoppers website at https://crimestoppers.nypdonline.org/ or on Twitter @NYPDTips.
All calls are strictly confidential.
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