During the last 20 years increasing experimental evidence has associated organic acid metabolism with plant tolerance to environmental stress. Current knowledge shows that organic acids not only act as intermediates in carbon metabolism but also as key components in mechanisms that some plants use to cope with nutrient deficiencies, metal tolerance and plant-microbe interactions operating at the root-soil interphase. In this review we summarize recent knowledge on the physiology and occurrence of organic acids in plants and their special relevance concerning nitrate reduction, phosphorus and iron acquisition, aluminum tolerance and soil ecology. We also discuss novel findings in relation to the biotechnological manipulation of organic acids in transgenic models ranging from cell cultures to whole plants. This novel perspective of organic acid metabolism and its potential manipulation may represent a way to understand fundamental aspects of plant physiology and lead to new strategies to obtain crop varieties better adapted to environmental and mineral stress.