Ketika pemerintah membentuk Gerakan Patriotik Tiga Mandiri untuk mengorganisasi gereja-gereja di bawah kendali partai pada tahun 1950, setahun setelah [[Revolusi Tiongkok (1949)|revolusi komunis]], Yuan dan banyak pendeta lainnya menolak untuk bergabung. Bersama dengan [[Wang Mingdao]] dan [[Watchman Nee]], pada tahun 1958 Yuan ditangkap dan dijatuhi hukuman penjara seumur hidup atas "kejahatan kontra-revolusioner".<ref>{{Cite BDCC|title=Allen Yuan|last= Doyle|first=G. Wright|url-id=yuan-allen|access-date=15 December 2018}}</ref>
[[Voice of the Martyrs]] mengutipnya berbicara mengenai saat ia berada di dalam penjara di [[Heilongjiang]], Tiongkokdi Timurlauttimur laut Tiongkok:<ref>{{Cite web|url=http://www.persecution.net/news/china84a.html|title=Allen Yuan Exchanges His Cross for a Crown|date=17 August 2005|website=The Voice of the Martyrs Canada|archive-url=https://web.archive.org/web/20080607073300/http://www.persecution.net/news/china84a.html|archive-date=7 June 2008|url-status=dead|access-date=8 June 2017}}</ref>{{blockquote|DuringSelama thosetahun-tahun yearsdi inpenjara, prisonistri mysaya wifemengalami sufferedkesulitan untoldyang hardshipstak interhitung bringingdalam upmembesarkan the childrenanak-anak. ISaya wasdikirim sentke todekat nearperbatasan theRusia Russianuntuk bordermelakukan doingpekerjaan farm workpertanian, growingmenanam ricepadi. [[Wang Ming-Dao|WangMingdao]] Mingdan Dao]]saya andpikir Ikami thoughtakan wemati wouldsebagai diemartir martyrsdi theresana.}}{{blockquote|In the labor camp it was very cold, food was bad, and the work was hard, but in 22 years I never once got sick. I was thin and wore glasses, but I came back alive; many did not. I also had no Bible for the 22 years and there were no other Protestant Christians there. I met only four Catholic priests. They were in the same situation I was in; they refused to join the [[Chinese Patriotic Catholic Association|Chinese Catholic Patriotic Association]].}}
