Bacterial cellulose nanocrystals (BCNCs) are biocompatible cellulose nanomaterials that can host guest nanoparticles to form hybrid nanocomposites with a wide range of applications. Herein, we report the synthesis of a hybrid nanocomposite that consists of plasmonic gold nanoparticles (AuNPs) and superparamagnetic iron oxide (Fe3O4) nanoparticles supported on BCNCs. As a proof of concept, the hybrid nanocomposites were employed to isolate and detect malachite green isothiocyanate (MGITC) via magnetic separation and surface-enhanced Raman scattering (SERS). Different initial gold precursor (Au3+) concentrations altered the size and morphology of the AuNPs formed on the nanocomposites. The use of 5 and 10 mM Au3+ led to a heterogenous mix of spherical and nanoplate AuNPs with increased SERS enhancements, as compared to the more uniform AuNPs formed using 1 mM Au3+. Rapid and sensitive detection of MGITC at concentrations as low as 10-10 M was achieved. The SERS intensity of the normalized Raman peak at 1175 cm-1 exhibited a log-linear relationship for MGITC concentrations between 2 × 10-10 and 2 × 10-5 M for [email protected]@BCNCs. These results suggest the potential of these hybrid nanocomposites for application in a broad range of analyte detection strategies.