In 1800, Abbé Paul returned to Rome and became the first Rector of the college from the Scottish secular clergy. After the fall of Napoleon Bonaparte, the Scottish bishops felt they no longer required the seminary in Rome but Abbé Paul strongly disagreed. He set about ensuring its survival, and with Papal support, forced the bishops to acquiesce.
In 1809 the college was involved in a dispute between Bonaparte and Pope Pius VII. The Pope was taken prisoner and Abbé Paul was obliged to lease out the college and vineyards. In 1811 he was expelled and returned to Huntly. However, in 1812 he was asked to return to Rome and act as the agent for the English and Scottish bishops. After a number of years of determined hard work, the doors of the college were opened in 1820 to receive five Scottish students.
At the age of 70 in 1827 Abbé Paul returned home to the Braes of Glenlivet. He fulfilled his life ambition of building a chapel for the people of the Braes. Abbé Paul had succeeded in saving a considerable sum of money and used it to build and furnish a chapel for his people of the Braes and Scalan. He obtained about 10 acres, The Faevait, from the Duke of Gordon and on this land St. Mary's chapel was erected in 1828. The building was able to accommodate 300 people. A house for the priest, substantial farm buildings and a cemetery were included. In 1832 a school was built and when this was burnt down in 1835 he paid for it to be rebuilt. As well as the furnishings, Abbé Paul gifted the vestments.
Pope Leo XII gave a silver gilt chalice in recognition of his service to the Papacy; this is now at Blairs Museum near Aberdeen and a photograph of it forms part of this display.
At the age of 78 in 1834 Abbé Paul returned to Rome. The Rector had died, the college closed and the students transferred to the College of Propaganda. He reopened the college within a year and remained in post until relieved in 1841. He retained an interest in the students until his death in 1846 and was buried in the Church of St. Andrew's of the Scots.
He was a man known for his diplomatic skills and determination, and the person who ensured the future of the Scots College Rome. He never forgot the people of the Braes and did everything in his power to ensure that the Catholic faith flourished and grew.