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Understanding the changing nature of the intraseasonal oscillatory (ISO) modes of Indian summer monsoon manifested by active and break phase, and their association with extreme rainfall events are necessary for probabilistic estimation of flood-related risks in a warming climate. Here, using ground-based observed rainfall, we define an index to measure the strength of monsoon ISOs and show that the relative strength of the northward-propagating low-frequency ISO (20–60 days) modes have had a significant decreasing trend during the past six decades, possibly attributed to the weakening of large-scale circulation in the region during monsoon season. This reduction is compensated by a gain in synoptic-scale (3–9 days) variability. The decrease in low-frequency ISO variability is associated with a significant decreasing trend in the percentage of extreme events during the active phase of the monsoon. However, this decrease is balanced by significant increasing trends in the percentage of extreme events in the break and transition phases. We also find a significant rise in the occurrence of extremes during early and late monsoon months, mainly over eastern coastal regions. Our study highlights the redistribution of rainfall intensity among periodic (low-frequency) and non-periodic (extreme) modes in a changing climate scenario.