How do I run two separate instances of Spyder

Update for Spyder 5.0.3+ (07/2021 onwards)

First, same as Carlos's answer:

Tools > Preferences

But then:

Application > Advanced settings

Then deselect [✔] Use a single instance, so it becomes [] Use a single instance, which will result in a new window opening each time Spyder is launched.

Still working for me in Spyder 5.1.5.

You can use the --new-instance option as well. Just run

spyder --new-instance

(Spyder maintainer here) This is easy. You need to go to:

Tools > Preferences > Application

in Spyder 5, or

Tools > Preferences > General

in Spyder 4, click the "Advanced Settings" tab, and deactivate the option called

[ ] Use a single instance

Then every time you start Spyder a new window will be opened. If you want the old behavior back, just activate that option again.