In 1926 he decided to stay in East Belarus after a conference in Minsk. After a couple of months he got arrested by the NKVD and sent to Solovki prison camp. He spent seven years in the Gulag and was exchanged for Branislaw Tarashkyevich, a West Belarusian politician held in Polish prison, in 1933.
Alyakhnovich's Gulag experience became a basis for his 1934 book of memoirs У капцюрох ГПУ (U kaptsyurokh HPU, In the claws of the GPU), that was later translated into several languages.
During the Second World War, Frantsishak Alyakhnovich was editor of the newspaper Беларускі глас (Byelaruski hlas, Belarusian voice) published in Vilnius. Apart from that, he was also one of the leaders of the Belarusian Independence Party - a Belarusian Christian Democratic underground antifascist organization led by padre Vincent Hadleŭski.
In 1944, Frantsishak Alyakhnovich was assassinated.