After his term as a Senator, Lowrie stayed on as Secretary of the Senate for eleven years. In 1836 he moved to New York City and went to work with the Missionary Board of the Presbyterian Church. He remained with them until his death. Three of his sons, John Cameron, Walter Macon, and Reuben, were prominent as missionaries to India and China. A nephew, Walter H. Lowrie, later served as chief justice of Pennsylvania's Supreme Court.
Lowrie died in New York City on December 14, 1868 (precisely 4 days after his birthday) and is interred in the First Presbyterian Church in Manhattan.
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