Abstract Organic soybean is presently less than 0.1% of total world production partly because of inappropriate fertiliser regime on degraded tropical soils. Therefore, two field trials were carried out during the late cropping seasons (June – November) of 2017 and 2018 to evaluate the agronomic performance of three soybean varieties: TGx 1448-2E, TGx 1835-10E and TGx 1989-9F as affected by foliar organic fertilisers: Arati Baja, Arati Nawoz, DI Grow, and soil applied organic fertiliser (Aleshinloye Grade B), and the control. The experimental design was Randomised Complete Block Design in a 3 × 5 factorial arrangement with three replications. Data were collected on yield attributes and seed yield of soybeans. Significant varietal difference (P < 0.05) in both years was recorded for number and weight of pods and seeds per plant, 100 seed weight, harvest index, and grain yield, except number of seeds per plant in 2018. Fertiliser × Variety interaction effect significantly (P < 0.05) affected above-ground plant weight and pod weight per plant in both years. On average, application of organic fertilisers resulted in grain yield (1.30–2.28 t/ha) comparable with Nigeria’s (0.97 t/ha) and Africa’s (1.37 t/ha) but lower than the world’s (2.85 t/ha) average values. The three foliar fertilisers and soil applied organic fertiliser enhanced seed yield of soybeans and are therefore recommended for soybean cultivation in the tropics.