Even if you play the organ just because you like it, it might be a good idea to practice several different compositions. I will explain why it is so. You see, because different historical periods, national schools, and composers require different performance practice techniques, playing different pieces every day will give you a benefit of diversifying your organ technique, too.
One possible approach would be to take 4 compositions: one free work by Bach, one chorale work by Bach, one Romantic work (Mendelssohn, Brahms, Frank etc.), and one Modern work (Messiaen, Langlais, Distler, Hindemith etc.)
The question then is: how to plan your practice time in order to learn these 4 works every day.
First of all, you need to know how much time you can spend practicing your music every day. 2 hours a day of practice would be a reasonable amount of time. Working less than that would not give the results you want for these 4 pieces. By the way, this does not necessarily mean that you have to spend 2 actual hours at the organ. It can involve some time at the piano, or even working without the instrument, too.
I would suggest practicing each piece for 30 minutes. In these 30 minutes, you can have time to do 2 things:
1) 10 minutes to practice and repeat the pages that you already have learnt before.
2) 20 minutes to learn new music from this piece.
If you do this with all 4 compositions regularly, after some time you will get to the point when you will know them all together.
Note, that if you want to play even more pieces every day, you have to spend more time practicing every day, too. In other words, if you have 10 compositions that you need to learn you will have to spend that much time every day practicing them. Of course, not all organ pieces have equal length and not all of them might have the same level of difficulty. Therefore, these numbers are relative. We have to adjust them to a real situation.
It is possible to practice four or five pieces one day and another four or five the next day, too. That way we just alternate our repertoire every other day.
So, would you like to be able to learn multiple organ pieces? Try this approach for yourself.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.