The development of microdose fertilization in West Africa on indigenous leafy vegetables (ILVs) is an alternative to nutrient management constraints. To overcome nutrient inefficiency, various application methods of urea (per hill, band/strip or uniform spreading of fertilizer dissolved in water) were tested on-station from 2015 to 2017 to identify the easiest and least time-consuming method of application. Several mineral fertilizers doses: 0, 10, 20, 30, 40, 60 with an incorporation of 5 t/ha manure (dry basis), and 40, 80 kg urea-N/ha without manure (half and full recommended rates, respectively) and farmers’ practice (FP, 100 to 120 kg/ha of NPK fertilizer and urea) were tested to determine the optimal microdose to be applied for sustainable production of ILVs. Two timings of application for the mineral fertilizer (at transplantation and 14 days after transplanting) were tested to identify the best timing. The methods of mineral fertilizer application by micro-dosing under Amaranthus cruentus L. showed similar performance in terms of fresh yield (FY), water productivity (WP) and economic gain. The early application of urea recorded a performance equivalent to the late one, giving market gardeners a sufficient time for effective application. Fertilizer micro-dosing application at 40 urea N/ha with manure improved significantly FY and WP compared to the control without mineral fertilizer and the recommended rate in contrast to Occimum gratissimum L. In farmer fields, the microdose at 60 kg/ha of urea gave similar performance in terms of FY yield compared to farmers’ practice for S. macrocarpon and O. gratissimum. Fertilization micro-dosing resulted twice in reduction of fertilizer application by producers in ILVs production. It is therefore necessary to widely disseminate this technique for the production of ILVs in Africa.