Indian summer monsoon exhibits significant intra-seasonal variations with active and break monsoon spells. Using MODIS data of 8 years (2000–2007), variations of cloud and aerosol properties over the Indian region associated with the active and break spells were examined. The study shows statistically significant variations of cloud properties (cloud optical depth, cloud fraction and cloud top pressure) between active and break monsoon days over central and northeast India and the equatorial Indian Ocean. During the monsoon break spells, associated with the anomalous circulation, aerosol loading from the north Arabian Sea is transported to central India. This increase in aerosol content decreases the cloud effective radii, suggesting the indirect effect of aerosols on cloud properties. There is also an inverse relationship of cloud properties over the monsoon zone over central India and the southeast equatorial Indian Ocean, suggesting possible role of southeast equatorial Indian Ocean on the development of active-break cycles.