How do I run two isolated instances of firefox?

You can use the Multifox extension in order to have two separate instances of Firefox that do not share cookies, but by still using only one profile.

Check out the profile argument like this:

firefox -profile "E:\myprofile"

Sorry about the windows file path ;) If you copy your main profile to a different profile, you will be starting a separate instance.

There's also one more possibility. You can execute the firefox command like:

firefox -P "profile-name" -no-remote

The option -no-remote disables remote control (i.e. control using the firefox command) of the new instance and logically it also implies the option -new-instance which is required to run a new isolated instance. It is also possible to use only the option -new-instance:

firefox -P "profile-name" -new-instance

Creating a new profile

firefox -ProfileManager -new-instance

The command will open an interactive window where you can manage existing profiles and create new ones. You can also start a new instance of Firefox using a selected profile. Be careful of the option "Use the selected profile without asking at startup" which is selected by default and which will make the selected profile to be the default one being used when starting firefox without -P.

Help

Excerpt from firefox -help:

  -P <profile>       Start with <profile>.
  -ProfileManager    Start with ProfileManager.
  -no-remote         Do not accept or send remote commands; implies -new-instance.
  -new-instance      Open new instance, not a new window in running instance.