One of the dispensaries in Barrio Logan and the other will be in Kearny Mesa.
So far, six dispensaries have been granted a permit, but only one has opened and it has been receiving positive reviews.
At Green Alternative in Otay Mesa, there is a 24-hour armed guard, bullet proof windows, and all patients walk through a metal detector before they can purchase medical marijuana.
"We are here to promote safe access for patients in need of medical grade cannabis," said Zachary Lazarus, A Green Alternative's general manager.
It's not what many would expect from a permitted medical marijuana shop that opened in March.
"We have some patients come in and say, wow, this is like a Nordstrom. This is incredible, how clean and nice this is," said Lazarus.
A Green Alternative is the first and only licensed and operational medical marijuana collective in San Diego.
In April 2014, the City Council approved an ordinance to start permitting these types of shops under strict regulations such as distance from schools, parks and children places.
So far, eight permits have been issued. One in Otay Mesa, San Ysidro, Barrio Logan, Midway, Pacific Beach, Mira Mesa and two in Kearny Mesa. Only four are allowed in each City Council District.
A Green Alternative fought many who thought this would be like an illegal pot shot: crime, druggies and nonsense.
City Council Member David Alvarez, whose district the dispensary is in, said he has not received a complaint.
Many of the shops with permits have not opened because they are going through appeals.