Habanero chillies (Capsicum chinense cv Habanero) are a popular species of hot chilli in Australia, with their production steadily increasing. However, there is limited research on this crop due to its relatively low levels of production at present. Rapid methods of assessing fruit quality could be greatly beneficial both for quality assurance purposes and for use in breeding programs or experimental growing trials. Consequently, this work investigated the use of infrared spectroscopy for predicting dry matter content, total phenolic content and capsaicin/dihydrocapsaicin content in 20 Australian Habanero chilli samples. Near-infrared spectra (908–1676 nm) taken from the fresh fruit showed strong potential for the estimation of dry matter content, with an R2cv of 0.65 and standard error of cross-validation (SECV) of 0.50%. A moving-window partial least squares regression model was applied to optimise the spectral window used for dry matter content prediction, with the best-performing window being between 1224 and 1422 nm. However, the near-infrared spectra could not be used to estimate the total phenolic content or capsaicin/dihydrocapsaicin content of the samples. Mid-infrared spectra (4000–400 cm−1) collected from the dried, powdered material showed slightly more promise for the prediction of total phenolics and the ratio of capsaicin-to-dihydrocapsaicin, with an R2cv of 0.45 and SECV of 0.32 for the latter. The results suggest that infrared spectroscopy may be able to determine dry matter content in Habanero chilli with acceptable accuracy, but not the capsaicinoid or total phenolic content.