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Permanent raised bed planting with crop residue retention is a form of conservation agriculture that has been proposed as an alternative to conventional tillage for wheat production systems in the Central Highlands of Mexico. A field experiment comparing permanent and tilled raised beds with different residue management under rainfed conditions was started at El Batán (State of Mexico, Mexico) in 1999. The percentage of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full crop residue retention (average for maize and wheat), while the percentages free microaggregates was lower. The percentages of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds with residue retention compared to permanent raised beds with removal of the residue (average for maize and wheat), while the percentages free microaggregates and silt and clay fraction was lower. Cultivation of maize significantly reduced the large macroaggregates, while wheat reduced the silt and clay fraction (average over all systems). Cultivation of maize reduced the C and N content of the free microaggregates compared to soil cultivated with wheat, while removal of plant residue reduced the C and N content of the silt and clay fraction compared to soil where residue was retained. The C and N content of the coarse particulate organic matter (cPOM) and microaggregates within the macroaggregates was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full residue retention, while C and N content of the cPOM was significantly lower when residue was removed or partially removed compared to the soil where the residue was retained. The δ 13C ‰ signatures of the macroaggregates, microaggregates, the silt and clay fraction, cPOM and microaggregates within the macroaggregates were not affected by tillage or residue management when wheat was the last crop, but removal of residue reduced the δ 13C ‰ signatures of the macro-, microaggregates and microaggregates within the macroaggregates significantly compared to soil where the residue was retained. Retaining only 30–50% of the organic residue still improved the soil structure considerably compared to plots where it was removed completely. Permanent raised beds without residue retention, however, is a practice leading to soil degradation. [ABSTRACT FROM AUTHOR]