Low concentration phosphorene-based sensors have been fabricated using a facile and ultra-fast process which is based on an exfoliation-free sequential hydrogen plasma treatment to convert the amorphous phosphorus thin film into mono- or few-layered phosphorene sheets. These sheets have been realized directly on silicon substrates followed by the fabrication of field-effect transistors showing the low leakage current and reasonable mobility for the nano-sensors. Being capable of covering the whole surface of the silicon substrate, red phosphorus (RP) coated substrate has been employed to achieve large area phosphorene sheets. Unlike the available techniques including mechanical exfoliation, there is no need for any exfoliation and/or transfer step which is significant progress in shortening the device fabrication procedure. These phosphorene sheets have been examined using transmission electron microscopy (TEM), Scanning electron microscopy (SEM), Raman spectroscopy and atomic-force microscopy (AFM). Electrical output in different states of the crystallization as well as its correlation with the test parameters have been also extensively used to examine the evolution of the phosphorene sheets. By utilizing the fabricated devices, the sensitivity of the phosphorene based-field effect transistors to the soluble L-Cysteine in low concentrations has been studied by measuring the FET response to the different concentrations. At a gate voltage of − 2.5 V, the range of 0.07 to 0.60 mg/ml of the L-Cysteine has been distinguishably detected presenting a gate-controlled sensor for a low-concentration solution. A reactive molecular dynamics simulation has been also performed to track the details of this plasma-based crystallization. The obtained results showed that the imparted energy from hydrogen plasma resulted in a phase transition from a system containing red phosphorus atoms to the crystal one. Interestingly and according to the simulation results, there is a directional preference of crystal growth as the crystalline domains are being formed and RP atoms are more likely to re-locate in armchair than in zigzag direction.