After three years Geddes was appointed rector of Scalan, the seminary hidden in the Braes of Glenlivet, founded in 1716, also forbidden by the spirit of the Penal Laws. It had gone through a bad patch. He established it as a centre of excellence in spiritual and academic terms and of human formation. The very building which was constructed under his supervision has been discovered by modern experts to be of the highest quality for the time. He even brought in the most up-to-date agricultural methods, because Scalan was part of a “fermtoun”