We present a microwave-assisted extraction procedure for lignin from woody and herbaceous biomass using a choline chloride−formic acid deep eutectic solvent (DES). A Box− Behnken experimental design was used to assess the influence of process parameters on the extraction performances. In addition to the gravimetric yield, two new experimental responses are proposed to evaluate the extraction efficiency and the structural integrity of extracted lignin. These responses were calculated by characterizing both the lignin extracts and the cellulosic residues by evolved gas analysis−mass spectrometry (EGA−MS) and analytical pyrolysis−gas chromatography/mass spectrometry (Py−GC/MS). Harsh extraction conditions (150 °C and 45 min) increased the extraction efficiency but provided lignins with lower structural integrity. Estimation of the extraction efficiency by Py−GC/MS data proved more reliable than that by gravimetric mass yield, as it was less affected by the presence of impurities and subproducts of the extraction process. The results show the potential of microwave-assisted DES extraction in providing lignin with tunable properties. The response parameters developed in this study provide a fast and reliable way to evaluate the extraction efficiency and the structural integrity of lignins extracted with DESs.