I like the Flor Peeters "Little Organ Book." It states that it is for beginners in organ playing and includes graded exercises on well-known hymn tunes. It lists for $14.95, but I think I only paid $10. for it online. If you follow it, your playing will improve.
I learned with, and have taught from First Organ Book, edited by Wayne Leupold. I highly recommend it for beginners. The format is easy to read, and even the beginning pieces are real music and not just exercise material.
The Gleason book can be used with beginners, but also has copious refresher information for even experienced organists. The content may be a little overwhelming for younger beginners, though.
The only exercises I ever had were a set of twelve by W. T. Best which my organ teacher copied out for her students. Attached are the first two, which I put into Finale a while ago for a friend. The rest cycle through the other keys, with the same bass-line, and increasing complexity of the manual parts. I remember that the challenge when I first started was getting my hands off the keys during the rests - I wanted to cling for balance!
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