I found the following methods:
background = 80/255*[1 1 1]; % Dark Gray
old_background_color = com.mathworks.services.Prefs.getColorPref('ColorsBackground'); % Get the current background color
com.mathworks.services.Prefs.setColorPref('ColorsBackground',java.awt.Color(background(1),background(2),background(3)))
com.mathworks.services.ColorPrefs.notifyColorListeners('ColorsBackground');
text = 190/255*[1 1 1]; % Light Gray
old_text_color = com.mathworks.services.Prefs.getColorPref('ColorsText'); % Get the current text color
com.mathworks.services.Prefs.setColorPref('ColorsText', java.awt.Color(text(1),text(2),text(3)))
com.mathworks.services.ColorPrefs.notifyColorListeners('ColorsText');
However, I get the following warning:
'com.mathworks' package and subpackages will be removed in a future release. There is no simple replacement for this.