Operating the swell pedal, foot coordination for the bass pedals, playing style, keeping track of your hands on two different manuals, etc. Also it depends on what you are accustomed to playing on an electronic keyboard and what you will be playing on the organ. Playing for Catholic Mass? Hymns? Boogie? Bluesy soulful gospel? Do you often play organ patches on your keyboard in a style typical of organists?
I'd say you could probably pass yourself off to the average listener, but an experienced organ player would be able to to tell you're out of your element. Bottom line: Dooooo iiiiiit and gain experience