He was the half-brother of architect and designer Edward Welby Pugin. He later began practice as the junior partner in Pugin & Pugin, the family architectural firm. When Edward Welby Pugin died suddenly on 5 June 1875 as a result of overwork and "injudicious use of chloral hydrate", the main responsibility for the practice passed to Peter Paul Pugin.
Although Peter Paul"s offices remained in London and Liverpool, his practice was largely Scottish, and he also maintained an office in Glasgow.
Apart from his own works, Peter Paul Pugin completed several of the works of Edward Welby Pugin after the latter"s death, in particular the church of Our Lady Star of the Sea in Workington, Cumbria. Peter Paul Pugin married Agnes, the third daughter of the Catholic builder John Bird of Hammersmith in 1886.
They had five children, but none entered the practice. Peter Paul Pugin was buried in Ramsgate.