Nowakowsky was born in Malyn in Ukraine in 1848, part of the Machnovska. Little of his early life is known, although there are several stories that survive. At 8 he left home, apparently due to the hounding of his stepmother, to sing in a trio with a cantor in the nearby town of Smelnik. He was later orphaned and joined the choir of cantor Spitzberg in Berditchev. He also studied traditional Jewish liturgical modes with cantor Yerucham (HaKaton) Blindman, and organ, theory and counterpoint at the Conservatory in Berdychiv.