Q. What does CMOS say regarding the use of accents in city names in Spanish? I’m specifically wondering about San José, Costa Rica. Do I keep the accent or get rid of it? What is the general rule?
A. Unless the city has a well-established English-language spelling—like Mexico City for Ciudad de México in Spanish, or Zurich for Zürich in German—retain any accents or other diacritical marks.
Merriam-Webster is a good source for determining whether a city has a common English-language spelling; you can usually use the first-listed spelling for any city entered there. The entry for San José includes the accent, so that’s your answer. (The entry for the city in Silicon Valley—San Jose, without an accent—doesn’t apply here.)
See also CMOS 14.30.