Vertical mixing modulates nutrient dynamics in lakes. However, surface warming reduces the range of vertical mixing and the probability of full circulation events. Important consequences of reduced vertical mixing include the sequestration of phosphorus (P) within a stagnant zone and the promotion of oligotrophication. Nevertheless, warming-induced shifts from full to partial mixing (meromixis) are not permanent and are partially reversible during exceptionally cold or windy winters. In this study, we investigated how intermittent meromixis affects lake P budgets. We examined the P cycle of a perialpine lake with variable mixing depths by pairing sedimentation and release flux measurements with sedimentary archives. We found that the amount of dissolved P surpassed that of the potentially mobile P in the sediments by a 13:1 ratio. At least 55% of the settled P was rapidly released to bottom waters isolated from flushing, illustrating the general biogeochemical mechanism that promotes deep-water P storage when lakes undergo warming. This storage process is abruptly inverted when meromixis suddenly retreats, deeper mixing introduces P pulses to the surface waters, thereby promoting phytoplankton proliferation. Our estimates showed that lakes containing up to 40% of the global freshwater volume could shift towards intermittent meromixis if the atmospheric warming trend continues. Thus, these lakes might accumulate 0-83% of their P load in irregularly circulating waters and are prone to large P pulses.