Instead, she moved to Kiev, where she joined the South Russian Workers' Union, founded by Nikolai Schedrin and Elizaveta Kovalskaya.
She formed an intense bond with Kovalskaya, who wrote in her memoirs that "I trusted Bogolomets completely; I knew she took things very seriously and - unlike some of the Kievans - strictly observed conspiratorial procedures.".
According to the American journalist George Kennan, who visited Siberia in the 1880s and interviewed political exiles, a warden named Colonel Soloviev had the two women stripped naked in his presence, then told their male comrades that they were "not much to look at.
Her husband, Alexander Mikhailovich Bogolomets (1850–1935) was in Paris in 1881, when he learnt of his wife's arrest, and returned illegally, intending to organise her escape.
Alexander himself was arrested in January 1882, and sentenced to a year and a half in prison, followed by exile to Tobolsk, where he was permitted to resume practising medicine.
Their son, Alexander Alexandrovich Bogolomets (1881–1946) was one of the leading medical academics of his generation, and President of the Ukraine Academy of Sciences in 1930 until his death.
Sofya's Sister, Olga, was another member of the South Russia Workers' Union, tried, imprisoned and deported with Bogomolets and Kovalskaya.