Nuclear Quadrupolar Resonance (NQR) is a radio frequency spectroscopy technique providing high resolution molecular analysis of solid materials containing quadrupolar atomic nuclei. The NQR technique does not necessitate an external magnetic field and, therefore, permits a large number of applications; it nevertheless suffers from relatively low sensitivity. The challenges of NQR instrumentation are therefore to increase its portability and sensitivity, and to limit interference from various noise sources (e.g., radio frequency interference) in order to perform field applications outside the laboratory. To address these challenges, we present a System-on-Chip Field-Programmable Gate Array (SoC-FPGA) based portable spectrometer integrating the major hardware elements of NQR instrumentation. These include : a high pulse width resolution pulse programmer, a fully controllable pulse transmitter, an acquisition module that performs detection, digital signal processing and storage of the acquired signal in an external memory, in addition to a hardware debugger. Pulser and acquisition Linux applications are embedded on the SoC-FPGA. While many recent compact spectrometers still have crucial radio frequency (RF) parts in the analog domain and lack performance optimization, most of our hardware and software modules are digitally implemented on SoC-FPGA. The designed portable spectrometer was successfully tested by detecting the expected frequencies of several samples such as NaNO2 , HMT or 1, 3, 5 − TCB covering hence the typical 14N and 35Cl NQR frequency ranges.