Ekaterina Antonenko studied choir conducting at the Moscow Academic Music College (Prof. Irina Usova) and Moscow Tchaikovsky Conservatory (Prof. Vladimir Sukhanov). In 2010–2012 Ekaterina was granted a DAAD scholarship for study at the Hochschule für Musik und Tanz Köln (Prof. Marcus Creed). In 2013 Ekaterina made her Ph.D. in musicology («Church music of Baldassare Galuppi»). From 2012 Ekaterina teaches at the Moscow Tchaikovsky Conservatory.

In 2011 upon the invitation of Peter Phillips Ekaterina conducted The Tallis Scholars in the Christ Church Cathedral, Oxford. In 2015 she assisted Hans-Christoph Rademann at rehearsals of the Penitential Psalms by Alfred Schnittke with the RIAS Kammerchor. Ekaterina instructed the Dresdner Kammerchor for the performance of Handel’s Alexander’s Feast at the Wratislavia Cantans festival 2015 and for the Commemorating concert of the Kristallnacht with works by Schnittke and Samuel Adler at the Frauenkirche, Dresden (2018). In 2019 Ekaterina instructed Europa Chor Akademie for the performance at the Martha Argerich Festival in Laeiszhalle (Hamburg) under Charles Dutoit. In 2022 she led the PaTRAM Male Choir concert tour in Israel. In 2022–2024 Ekaterina was the head of the Perm Opera and Ballet Theatre Choir, in 2024 she assumed the role of Artistic Director and Principal Conductor of the Sveshnikov State Academic Russian Choir.