| B |
| Barnes & Noble | La Jolla Village, no street on record | | | |
| Barnes & Noble | 10775 Westview Parkway, Mira Mesa Gateway | stores.barnesandnoble.com | +1-858-684-3166 | |
| Barnes & Noble | 7610 Hazard Center Drive, Mission Center | store-locator.barnesandnoble.com | | |
| Barnes & Noble | 11744 Carmel Mountain Road, Carmel Mountain Ranch | | | |
| Book Nook | 12911 Pacific Place, Pacific Highlands Ranch Village | | | |
| Book Off! | 4240 Kearny Mesa Road, Convoy District | bookoffusa.com | +1-858-627-9600 | |
| Book Tree | 3316 Adams Avenue, Normal Heights | thebooktree.com | +1-800-700-8733 | |
| Bookstar/Loma Theatre | 3150 Rosecrans Place, Loma Portal | store-locator.barnesandnoble.com | | |
| Buddha's Light Book Storenot edited since 2022 | University Heights, no street on record | | | |
| C |
| Comic-Kazenot edited since 2014 | East Clairemont, no street on record | | | |
| D |
| D. G. Wills | 7461 Girard Avenue, La Jolla | | | |
| F |
| Footnote Books | 1627 University Avenue, University Heights | | | |
| Friendly Finds Bookstore | Del Mar Highlands, no street on record | | | |
| Friends of the Mira Mesa Library Book Sale Room | Mira Mesa, no street on record | | | |
| G |
| Goodwillnot edited since 2012 | University Square, no street on record | | | |
| L |
| La Playa Books | 1026 Rosecrans Street, Roseville | laplayabooks.com | +1 619-226-2601 | |
| Library Shop Mission Hills | 925 West Washington Street, Uptown Medical Complex | libraryfoundationsd.org | | |
| M |
| Mysterious Galaxy Bookstore | 3555 Rosecrans Street, Midway District | mystgalaxy.com | +1-619-539-7137 | |
| P |
| Pennywise Books | 1331 Garnet Ave, Pacific Beach | | | |
| R |
| Rising Sun Creationsnot edited since 2013 | Mission Valley, no street on record | | | |
| S |
| San Ysidro Branch Library | 4235 Beyer Boulevard, El Pueblito Viejo | sandiego.gov | +1-619-424-0475 | |
| San Ysidro Friends of the Library Book Storenot edited since 2021 | El Pueblito Viejo, no street on record | | | |
| sandiweb | 5185 Luigi tre, Tierrasanta Town Center | sandiweb.com | +1-800-518-1233 | |
| SDSU Bookstore | Montezuma Mesa, no street on record | shopaztecs.com | +1-619-594-7525 | |
| Southern California Comics | 8280 Clairemont Mesa Boulevard, Kearny Mesa | | | |
| T |
| The Book Catapult | 3010-B Juniper Street, Burlingame | thebookcatapult.com | +1-619-795-3780 | |
| The Jerry Peterson Friends of the Library Bookshop | Rancho Bernardo, no street on record | | | |
| The Torrero Storenot edited since 2015 | Silver Terrace, no street on record | | | |
| U |
| UC San Diego Bookstore | 9500 Gilman Drive, La Jolla Farms | ucsandiegobookstore.com | +1-858-534-7326 | |
| Upstart Crow bookstore & cafe | 835 C West Harbor Drive, Marina | upstartcrowtrading.com | | |
| V |
| Verbatim Books | 3793 30th Street, North Park | verbatimbooks.com | +1 619-501-7466 | |
| W |
| Warwick's | Village of La Jolla, no street on record | | | |
| Warwick'snot edited since 2022 | Liberty Station, no street on record | | | |
| West Grove South Parknot edited since 2017 | 3010 Juniper Street, Burlingame | | | |
| Y |
| Yesteryear Comics | 9353 Clairemont Mesa Boulevard, Spectrum Center | | | |