An integrated real-time sensing system that uses a portable Raman spectrometer and a micropillar array chip has been developed for field analysis. The problem of poor detection sensitivity, caused by miniaturization in the portable Raman spectrometer, was overcome by using the surface-enhanced Raman scattering (SERS) technique. The problem of poor reproducibility in the SERS detection, caused by different particle sizes and inhomogeneous degrees of aggregation, was also overcome by using continuous flow and homogeneous mixing between the analytes and nanocolloidal silver in a micropillar array microfluidic chip. Two hazardous materials, dipicolinic acid and malachite green, were quantitatively analysed using our integrated portable Raman sensor system. The observed limit of detection was estimated to be 200 ppb and 500 ppb, respectively. Our proposed analytical method, using a micropillar array PDMS chip and a portable SERS system, offers a rapid and reproducible trace detection capability for hazardous materials in the field.