Transparent wood (TW) is an interesting polymer biocomposite with potential for buildings and photonics applications. TW materials need to be eco-friendly and readily processed with few defects, for high optical transmittance and low transmission scattering at wide angles (haze). Two wood templates with different lignin-content are impregnated with a new thiol–ene thermoset system. The more eco-friendly bleached wood template results in transparent wood with high optical transmission and much reduced transmission haze, due to strong reduction of interfacial air gaps. Characterization includes template composition, thiol–ene distribution, and polymerization in wood cell wall by EDX and confocal Raman microscopy, also NMR and DSC, tensile testing and FE-SEM fractography for morphology and wood/thiol–ene interface adhesion assessment. The wood template is a true nanocomposite with thiol–ene polymer located inside the nanoporous wood cell wall. Advanced TW applications require not only appropriate wood template modification and careful polymer matrix selection but also tailoring of the process to impregnation and polymerization mechanisms, in order to reduce optical defects.