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Summary Frequent applications of chicken manure to a volcanic‐ash soil resulted in an increased crop yield several years after the applications ceased. Improved nutrient cycling through the soil organic matter (SOM) was thought be the cause of this. An area that for several years had been under either unimproved fallow or continuous bean‐maize intercropping (with chicken manure application) was planted with maize intercropped with the legume Arachis pintoi. Soil samples were fractionated into several sizes of aggregates and incubated for 6 weeks in intact form and after crushing the aggregates. Between 1.2 and 3.1% of the C in any aggregate size class exited in easily decomposable (i.e. not physically or chemically protected) form. Less than 0.8% of the macroaggregate C was physically protected by the aggregate structure. More than 97% of the C in any aggregate size class can be considered resistant. The large‐or small‐macroaggregate‐protected SOM (i.e. in aggregates > 2000 μm and 250–2000 μm, respectively). once made available, was more easily decomposed than the unprotected SOM. The large SOM content (45.8–57.3 g C kg−1) but yet limited mineralizability indicates that mechanisms other than soil macroaggregation are important for protecting SOM in this soil. Binding of organic molecules onto allophane minerals is likely to be such a mechanism. The larger yield and nutrient uptake by the maize in the former bean‐maize plots compared with the former fallow plots could not be explained by differences in SOM decomposition. We think that the frequent application of chicken manure to the former bean‐maize plots increased the available phosphorus in these strongly P‐sorbing soils by increasing the cycling of organic‐P or by blocking some of the P‐reactive sites. This, however, needs to be further investigated.