The detection of chlorinated hydrocarbons by Curiosity on Mars has been attributed to the presence of unidentified indigenous organic matter. Similarly, oxychlorines on Earth have been proposed to be responsible for the apparent lack of organics in the Atacama Desert. The presence of perchlorate (ClO₄⁻) poses a unique challenge to the measurement of organic matter due to the oxidizing power of oxychlorines during commonly used pyrolysis–gas chromatography–mass spectrometry (py-GC-MS) methods. Here, we show that perchlorates and other oxyanion salts inhibit the detection of organic compounds but that removing these problematic species prior to pyrolysis by using an optimal sample extraction duration and suitable ratios of water to sample mass enables analysis. We have characterized leached and unleached samples containing perchlorates from the Atacama Desert and have found that after leaching, the py-GC-MS chromatograms of the dried mineral residues show identifiable biomarkers associated with indigenous cyanobacteria. Samples which were pyrolyzed without leaching showed no detectable organic matter other than background siloxane and very weak or no trace of detectable polychlorinated benzenes. Dried sample residues remaining after leaching, the mineral matrix and water-insoluble organic matter, showed a strong organic response in all cases when analyzed by py-GC-MS. These residues are most likely the product of the pyrolysis of water-insoluble organics originally present in the samples. In addition, our results imply that previous soil analyses which contained high levels of oxyanions and concluded that organics were either not present or were present at extremely low levels should be reexamined.