Energetic processing methods such as hyperthermal implantation hold special promise to achieve the precision synthesis of metastable two-dimensional (2D) materials such as Janus monolayers; however, they require precise control. Here, we report a feedback approach to reveal and control the transformation pathways in materials synthesis by pulsed laser deposition (PLD) and apply it to investigate the transformation kinetics of monolayer WS2 crystals into Janus WSSe and WSe2 by implantation of Se clusters with different maximum kinetic energies (<42 eV/Se-atom) generated by laser ablation of a Se target. Real-time Raman spectroscopy and photoluminescence are used to assess the structure, composition, and optoelectronic quality of the monolayer crystal as it is implanted with well-controlled fluxes of selenium for different kinetic energies that are regulated with in situ ICCD imaging, ion probe, and spectroscopy diagnostics. First-principles calculations, XPS, and atomic-resolution HAADF STEM imaging are used to understand the intermediate alloy compositions and their vibrational modes to identify transformation pathways. The real-time kinetics measurements reveal highly selective top-layer conversion as WS2 transforms through WS2(1–x)Se2x alloys to WSe2 and provide the means to adjust processing conditions to achieve fractional and complete Janus WSSe monolayers as metastable transition states. The general approach demonstrates a real-time feedback method to achieve Janus layers or other metastable alloys of the desired composition, and a general means to adjust the structure and quality of materials grown by PLD, addressing priority research directions for precision synthesis with real-time adaptive control.