We demonstrate a novel technique for quantitative detection of carbon nanotubes (CNTs) in biological samples by utilizing the thermal response of CNT under microwave irradiation. In particular, rapid heating of CNT due to microwave absorption is employed to quantify CNT uptake in agricultural samples with excellent sensitivity. We inject alfalfa (Medicago sativa) roots with a known quantity of CNT (single-walled and multi-walled) and expose the samples to a microwave field (30-50 W) to generate standard temperature-CNT concentration relationships; this detection method is then used to accurately determine CNT uptake by alfalfa plant roots grown in CNT-laden soil. The threshold for detectable CNT concentration is much lower (<0.1 μg) than common analytical methods such as electron microscopy and Raman spectroscopy. Considering the lack of effective detection methods for CNT uptake in plants, our concept is not only unique but also practical, as it addresses a major problem in the field of nanomaterial characterization and nanotoxicology risk assessment.