Increasing population density and food needs in the Sahel are major drivers behind the conversion of land under natural vegetation to arable land. Intensification of agriculture is a necessity for farmers to produce enough food. As manure is scarce and fertilizers expensive, this study looks into the potential role of cowpea (Vigna unguiculata L.) and short duration fallow in maintaining soil fertility and productivity and in reducing the major weed problem Striga hermonthica (Del.) Benth. The research was carried out ‘on-farm’ in a traditional millet (Pennisetum glaucum (L.) R.Br.) growing area in the Malian Sahel, near Bankass. The four year experiment combined 0, 2, 5, and 7 years of preceding fallow with (i) 4 years of millet, (ii) 1 year of cowpea + 3 years of millet, and (iii) 1 year of cowpea + 3 years of millet/cowpea inter-cropping. Total millet production (4 years) was 1440 kg ha−1 for all systems with 2, 5 or 7 years of preceding fallow against 1180 kg ha−1 for systems without fallow. Cowpea grain production showed no significant differences between fallow treatments. Over 4 years, all cropping systems produced similar total amounts of millet grain, implying that the millet ‘lost’ during the year with a pure cowpea crop in treatments (ii) and (iii) was compensated within three years, while the cowpea grain production was an additional benefit. Such compensation was however not observed for increasing number of preceding fallow years, showing that there is no additional production benefit in 5-7 years of fallow as compared to 2 years. The soil organic carbon content decreased more slowly in treatments with a cowpea pure crop in 1998 than in the millet pure crop, while overall higher contents were observed after preceding fallow also after four years of cropping. Striga hermonthica infestation decreased linearly with duration of preceding fallow, but also after seven years of fallow and one year of cowpea the hemi-parasitic weed still re-appeared. Overall the intensification through a cowpea pure crop and cowpea intercrop in these millet-based systems improved production and a number of other characteristics of the system, making it more viable.