Summary Stable isotopes are extensively used as tracers for the study of plant‐water sources. Isotope‐ratio infrared spectroscopy (IRIS) offers a cheaper alternative to isotope‐ratio mass spectroscopy (IRMS), but its use in studying plant and soil water is limited by the spectral interference caused by organic contaminants. Here, we examine two approaches to cope with contaminated samples in IRIS: on‐line oxidation of organic compounds (MCM) and post‐processing correction. We assessed these methods compared to IRMS across 136 samples of xylem and soil water, and a set of ethanol– and methanol–water mixtures. A post‐processing correction significantly improved IRIS accuracy in both natural samples and alcohol dilutions, being effective with concentrations up to 8% of ethanol and 0.4% of methanol. MCM outperformed the post‐processing correction in removing methanol interference, but did not effectively remove interference for high concentrations of ethanol. By using both approaches, IRIS can overcome with reasonable accuracy the analytical uncertainties associated with most organic contaminants found in soil and xylem water. We recommend the post‐processing correction as the first choice for analysis of samples of unknown contamination. Nevertheless, MCM can be more effective for evaluating samples containing contaminants responsible for strong spectral interferences at low concentrations, such as methanol.