Nanomaterials use in traditional spectroscopic assays has enabled the development of more sensitive and accessible methods with wider-range of applications. Usually, the sensitivity of nanosensors is improved through the incorporation of labels or by inducing nanoparticles aggregation. Herein, we present the development of a label-free, selective, reliable, and affordable gold nanoprisms aptasensor to detect the content of ochratoxin A (OTA) in suspension by surface-enhanced Raman spectroscopy (SERS). Label-free SERS provides a molecular signature of the aptamer-OTA complex used and enables to discriminate OTA solutions from 10 to 250 ppb (25–620 nM) with multivariate analysis. This label-free nanoaptasensing system represents a new possibility for simpler and more reliable and accessible procedures for OTA determination.