Fertilisation using animal manure can improve soil structure. However, the positive and negative effects of this practice remain inconclusive, and manure application can change the superficial electric potential, thereby increasing the dispersible clay content, disaggregation and susceptibility of soil to erosion and contamination of surface water. The objective of this study was to evaluate a water-dispersible clay and the aggregation of an oxisol over time with the application of different doses of swine and poultry manure. The experiment was conducted in a very clayey dystroferric red latosol, and the treatments consisted of the superficial application of 33 and 66 m3 ha−1 swine manure and 1920 and 3840 kg ha−1 poultry manure for corn production. A treatment without fertiliser (mineral or organic) was used as a reference. Soil samples from 0.00 to 0.10 m layer were collected at 0, 15, 30 and 60 days after manure application to determine the soil aggregate classes, weighted mean diameter (WMD), aggregate stability index, dispersible clay content, pHH2OpHH2O and pHKCl. The ΔpH was also determined. The application of swine manure led to rapid and dynamic changes in the dispersible clay content as well as the aggregation process compared to the application of poultry manure. The effects of the application of 33 or 66 m3 ha−1 swine manure can be divided into three phases: (i) immediate increases in the pHH2OpHH2O resulting in an increase in dispersible clay content and the mass of aggregates <0.250 mm immediately after the application of the manure at 0 days after application (DAA); (ii) a decrease in the pHH2OpHH2O as well as flocculation and restructuring of the soil between 15 and 30 DAA; and (iii) a further increase in the mass of aggregates <0.250 mm between 30 and 60 DAA. In contrast to the swine manure applications, a cementation effect of organic carbon was observed in the poultry manure applications, and clay flocculation and soil aggregation occurred after the application of 1920 kg ha−1 or 3840 kg ha−1 poultry manure, thereby increasing the WMD at 15 DAA. However, the aggregation effect was ephemeral, and at 30 and 60 DAA, decreases in the WMD and aggregates >2.00 mm were observed independent of the doses of applied poultry manure.