The oxygen isotope ratio of phosphates is a powerful tool to study phosphorus in the soil‐plant system. In the past two decades, the scientific community has made substantial progress in characterizing biogeochemical processes that lead to an alteration of oxygen isotope ratios in phosphates and in evaluating oxygen isotope ratios of phosphates in plants and soils under various environmental conditions around the globe. However, there are still uncertainties with respect to their interpretation in environmental systems. These uncertainties include the comprehensive analysis of isotope endmembers, artifacts during the chemical extractions and the phosphate purification protocols, overlapping isotope values from various processes and sources, gaps of knowledge about isotope effects of metabolic pathways, and the possibly erroneous assumption that insights from experiments under controlled laboratory conditions can be directly translated into the complex soil‐plant system. This paper provides a critical discussion of these uncertainties addressing recommendations and needs for future research and gives an outlook on recent technological advances, such as triple oxygen isotope analysis or the use of High Resolution Mass Spectrometry. We conclude by suggesting that a concerted and systematic effort by scientists from a wide range of disciplines will be necessary to remove the uncertainties in the interpretation of oxygen isotope ratios in phosphates as an environmental tracer.This article is protected by copyright. All rights reserved.