Phosphorus (P) is a major agricultural nutrient and, in its mineable form, a potentially scarce resource. Countries with limited physical access to P should hence develop an effective national P governance. This requires analyses of trends and variations in P flows and stocks over time. Here, we present a long‐term P flow analysis for the Indian agri‐food sector from 1988 to 2011. Major P flows are imports of mineral P, fertilizer application, and uptake of animal fodder. The mineral P import dependency ratio is constant at around 93%. On average, 20% of P inputs to soils are lost through erosion. Key drivers of changes in P flows include population growth, dietary change, and agricultural intensification. To reduce its P fertilizer import dependence, India could, for example, substitute up to 19% of the presently applied mineral P if manure used as a household fuel were recycled, and up to 21% if P was fully recovered from wastewater and household waste. Comparing selected indicators for P use in agriculture with China and the European Union (EU) reveals that there are structural similarities, such as increasing fertilizer application rates and P accumulation in soils, with the first but large differences compared to the latter. The analyses highlight that in contrast to static indicators, the time‐continuous tracking of P flows provides substantial advantages, such as the identification of long‐term trends, drivers, and intervention options for sustainable P management, given that it allows for the interpretation of present indicators in the context of past trends and legacies.