Productivity, profitability and partial nutrient balance in maize-based conventional and organic farming systems in Kenya

•Maize based farming systems were compared for 6 years in Chuka and Thika in Kenya.•High input organic system yields equal to conventional except in year 1 at Thika.•Maize-bean intercrop in low input organic systems yielded as conventional one.•High and low input organic production costs were higher than conventional ones, but.•From year 5 organic was more profitable than conventional in the high input systems.•Conventional systems exported more nutrients than organic systems.