The complete valorisation of sugar beet pulp (SBP) through pectooligosaccharides (POS) extraction and biobutanol production was studied. A central composite experimental design was planned to optimise the time and temperature of the hydrothermal microwave-assisted extraction. 59.7% of the POS present in the SBP were recovered, and a prehydrolysate with 31.1 g POS/L was obtained under optimal conditions (165 °C and 12 min). The prehydrolysate was further precipitated by ethanol. One-step and stepwise alcohol precipitation were evaluated. The prehydrolysate:ethanol ratio was increased from 1:1–1:3 in the stepwise precipitation, whereas a ratio of 1:2 was used in the one-step precipitation. The pectin fractions differed from each other in their chemical composition. The molecular weight of the pectin fractions ranged from 474 to 523 kDa, and the degree of esterification of all of them was higher than 50%, so they can be considered high methoxyl pectins. On the other hand, the pretreated solid enriched in glucan was subjected to enzymatic hydrolysis with cellulases and fermented by Clostridium beijerinckii, producing 8.3 g butanol/L after 48 h of fermentation (53 kg butanol/t SBP). As this research has demonstrated, SBP is a suitable feedstock for a green biorefinery approach. The fractionation of SBP by hydrothermal treatment avoids using acid and alkaline solvents and allows high POS and biobutanol production yields.