When you change the default cookie "lifetime" from "Keep until: they expire" to "Keep until: I close Firefox", Firefox changes any persistent cookies that sites set to session cookies. To allow a site to set a persistent cookie, you need to make an exception (site permission).

When you turn on the clearing of history at shutdown and include cookies, that runs a completely separate process which does not pay any attention to cookie lifetime or exceptions (site permissions). It just nukes them all.

Note that some cookies might survive clearing at shutdown if they are encoded into your session history file, the one Firefox uses to restore your previous session windows and tabs. I haven't tested.

Let all cookies expire when Firefox is closed to make them session cookies.

• Firefox/Tools > Options > Privacy > "Use custom settings for history" > Cookies: Keep until: "I close Firefox"

Create a cookie 'allow' exception for cookies that you would like to keep.

• Firefox/Tools > Options > Privacy > "Use custom settings for history" > Cookies: Exceptions

Clearing "Site Preferences" clears all exceptions for cookies, images, pop-up windows, software installation, passwords, and other website specific data.

Clearing cookies will remove all specified (selected) cookies including cookies with an allow exception that you would like to keep.

• Tools > Options > Privacy > Firefox will: "Use custom settings for history": [X] "Clear history when Firefox closes" > Settings
• https://support.mozilla.org/kb/remove-recent-browsing-search-and-download-history

Both answers were completely satisfactory. Although the unchosen answer is a little nicer organized, the chosen answer contains an extra piece of information that helped me to better understand how Firefox handles clearing cookies: i.e., there may still be some cookies that are not deleted from the session history.

From what I understand, the only functional difference between changing the cookie expiration date and telling the browser to clear cookies with history on close, is that the latter will bypass exceptions?

So if I always want all cookies deleted I should clear cookies with history when firefox closes. If I want to set any exceptions I need to use the setting to change the default expiration for cookies to when the browser closes.

You can't use exceptions if use "Clear history when Firefox closes" because that removes all the cookies whether they have an allow exception or not. Cookies stored as part of session data may still be kept if you use "Clear history when Firefox closes" and there is an allow exception.

You can set the browser.sessionstore.privacy_level pref to 2 (never) or 1 (non-HTTPS) on the about:config page to disable saving cookies via session restore in the sessionstore.js file. The browser.sessionstore.privacy_level_deferred pref is used when you do not reopen the previous session automatically via "Show my windows and tabs from last time" and uses the same values.

• http://kb.mozillazine.org/browser.sessionstore.privacy_level