With the recent changes in the Prezi edit mode layout, it might be quite difficult to find how to change the background color at first. The option is now hidden behind 2 menus and a scroll to the bottom of 1 sidebar.
To change the background you have to:
1) Click on the Customize button at the top center of the screen.
2) Scroll down to the bottom in the sidebar that appeared
3) Click the Advanced button
4) The Theme Wizard will open, allowing to enter an RGB code for the background color. Use this link to generate RGB code for any color.
5) Alternatively you can click the Wizard button which allows to choose between a small amount of predefined colors.