In this work, different lignins were obtained from two different extraction methods (kraft and organosolv) but from the same raw material (Eucalyptus globulus sp.). They were subsequently fractionated to determine the differences of each extraction method and their corresponding physicochemical properties found in fractionation sequence and obtained fractions. The goal of the fractionation was to obtain lignin fractions with narrower molecular weight distribution and lower polydispersity index (PI). The solvent sequence was designed based on the environmental friendly properties, health and safety assessments of the selected organic solvents: (methanol (MeOH), ethanol (EtOH), propan-2-one (DMK), ethyl acetate (EtOAc), propan-1-ol (nPrOH), propan-2-ol (iPrOH), butan-2-one (MEK), and butan-1-ol (tBuOH)). The different fractions obtained were characterised to determine their chemical structure by several analytical techniques, such as Fourier Transformed Infrared Spectroscopy (FTIR), Ultraviolet (UV), Phosphorus-31 Nuclear Magnetic Resonance (31P NMR), Pyrolysis–Gas Chromatography/Mass Spectrometry (Py-GC/MS), Thermogravimetric analysis (TGA), and Differential scanning calorimetry (DSC). In addition, Gel Permeation Chromatography (GPC) was used to obtain the molecular weight distribution. This study showed an effective method for obtaining homogeneous lignins with specific structures and properties depending on the solvent and molecular weight attained. Moreover, the method designed was found to be effective regardless of the lignin extraction process employed; besides, various lignin fractions were obtained which were different from each other, having specific target applications depending on their structure and chemical properties, ranging from small molecules with abundant reactive sites to act as active materials or copolymer reagents for many applications, to larger and more inactive molecules with higher thermal resistivity.