See the following link for an Information Bulletin IB-400 prepared by the City of San Diego. This is a comprehensive summary of the regulations for ADU builders in the City of San Diego as well as JADUs.
Generally, the City regulations are very similar to others in the county, however, the City regulations include an ADU Bonus Program. One Bonus ADU is allowed for every ADU that is set aside as affordable to very low-income and low-income households for at least 10 years, or as affordable to moderate-income households for at least 15 years, guaranteed through a written agreement and a deed of trust securing the agreement.
Applications for Building Permits for ADU’s require the payment of plan check and inspection fees regardless of whether or not a Permit Ready Building Plan has been utilized. School Fees are required if the project exceeds 500 sf. Your ADU may be exempt from Development Impact Fees and you need to check the regulations to be sure.
Most projects within the Coastal Overlay Zone require the approval of a Coastal Development Permit. There are certain exemptions that may be available.