An analytical methodology was developed for detection of malathion in the peels of tomatoes and Damson plums by surface-enhanced Raman imaging spectroscopy and multivariate curve resolution. To recover the pure spectra and the distribution mapping of the analyzed surfaces, non-negative matrix factorization (NMF), multivariate curve calibration methods with alternating least squares (MCR-ALS) and MCR with weighted alternating least square (MCR-WALS) were utilized. Error covariance matrices were estimated to evaluate the structure of the error over all the data. For the tomato data, NMF-ALS and MCR-ALS presented excellent spectral recovery even in the absence of initial knowledge of the pesticide spectrum. For the Damson plum data, owing to heteroscedastic noise, MCR-WALS produced better results. This methodology enabled detection below to the maximum residue limit permitted for this pesticide. This approach can be implemented for in situ monitoring because it is fast and does not require extensive manipulation of samples, making its use feasible for other fruits and pesticides as well.87924-33