This study examines whether organic fertiliser systems can improve both productivity and profitability in tissue-cultured Lakatan banana (Musa acuminata Colla) production under smallholder conditions. It tests the hypothesis that organic fertilisers can deliver a superior balance between agronomic performance and return on investment (ROI) compared to conventional fertiliser regimes. This is critical given rising synthetic fertiliser costs and increasing pressure to adopt environmentally sustainable practices. Using a randomised complete block design under field conditions, multiple organic fertilisers were evaluated relative to synthetic inputs across growth and yield indicators. Results showed that chicken manure produced the highest bunch weight (13.9 kg) compared to the control (6.0 kg), while cattle manure and vermicast also demonstrated competitive performance in vegetative growth and yield components. These findings indicate that organic fertilisers exhibit functional complementarity, where specific inputs enhance different growth stages, enabling competitive yield performance without reliance on costly synthetic fertilisers. The study’s key contribution is the integration of soil health management and economic viability, demonstrating that locally available organic inputs can reduce fertiliser costs while maintaining productivity. This presents a viable pathway for improving farm profitability and investment attractiveness. These results support the adoption of organic fertilisation to sustainably enhance Lakatan banana productivity, while highlighting its potential as an alternative, eco-friendly model for sustainable agriculture.