Alley-cropping has successively been overestimated and despised, due to unrealistic expectations of this “more natural” type of agriculture and the disappointment thereafter, when the negative effects of trees on crops became evident over time. In this paper we examine the performance and underlying mechanisms of a Calliandra (Calliandra calothyrsus Meissn.)–maize (Zea mays L.) alley-cropping system on a phosphorus (P) limiting Ferralsol in Western Kenya. The system performance analysis methods of [The ‘dark side’ of intercropping: manipulation of soil resources. In: Sinoquet, H., Cruz, P. (Eds.), Proceedings of the International Conference on Ecophysiology of Intercropping. INRA, Paris, France, pp. 45–66] and [Agric. Ecosyst. Environ. 80 (2000) 87] were used as well as mechanistic research into availability, uptake and balances of below ground resources. The Calliandra–maize system performed worse than sole maize (I=?66%, according to Ong’s method) Calliandra affected the less limiting resource nitrogen (N) positively, but the negative effect of Calliandra on P-availability, the main limitation of the environment outweighed the positive or fertility effect, according to Kho’s performance analysis method. However, after P application, when the main limiting resource for maize in our environment shifted to N, the Calliandra had still only a marginal positive effect on maize yields (insignificant 5% increase of alley-cropping compared to sole maize). This was explained by a negative total N balance in the soil of ?30 kg ha?1, and a negative inorganic N balance in the soil of ?277 kg ha?1 over the seven seasons. The difference between total and inorganic N balance was due to a mineralisation of only 20% of the N in all the Calliandra mulch applied over the seven seasons. Net negative nutrient balances also explain the general trend of decreasing yields of 40–90% over the seven seasons. We conclude that the combination of Ong’s simple method, Kho’s resource-based explanation and further investigation of long-term supply and availability of the resources that are the main limitation(s) of an environment can give an understanding needed to create productive and sustainable alley-cropping systems.