This study reports on the use of surface-enhanced Raman scattering (SERS) detection and follow-up treatment of Paracoccidioides brasiliensis (Pb) infection in lung's mice. We also reports on the introduction of a new drug carrier system [nanoparticle-Amphotericin B (NP-AmB)], comprising magnetic NP surface functionalized with AmB, and its use in the treatment of infected and non-infected mice. SERS was successfully used to monitor the efficacy of the mice's treatment using the new NP-AmB, while free AmB (F-AmB), considering the current drug of choice for treatment of Pb infection, was also used and taken as reference for the treatment. We found SERS provides a robust platform to discriminate infected lung tissues from non-infected ones based on fingerprints assessed via SERS spectra and focused on the redox state of heme groups present in the collected biological material. Finally, SERS data reported in this study indicated that the new NP-AmB formulation provides similar clinical response as the F-AmB, although incorporating 40% lower content of AmB and administered in a time interval schedule (every 72 h) three times longer than F-AmB (every 24 h). Copyright © 2013 John Wiley & Sons, Ltd.