This article seeks to understand the challenges of literacy acquisition under the Thematic Curriculum reform in Uganda, which introduced Mother Tongue instruction in lower primary. We compare teachers' perspectives from two central districts using Luganda and two peripheral districts using Ateso, drawing on a multi-layered approach to understand the interplay between policy, pedagogical, and conceptual-level factors that shape the way Mother Tongue instruction is implemented. We show how teachers cope with the challenges of parallel literacy instruction in two languages against the dilemma of which language to prioritise. By focusing on teachers' agency, we suggest that teachers' language choices demonstrate the bilingual realities of Ugandan schools and societies, which undermine either/or narratives that pit English and local languages against each other. Our main contribution is in exposing teachers' unofficial classroom practices and relating these to an interplay between micro- and macrolevel factors.