The pectin from the cell walls of olive waste (alperujo) and apple, orange and strawberry fruits was extracted using choline chloride (ChCl) and the yield and chemical and structural compositions were compared to pectin extracted using citric acid (CA) and ammonium oxalate/oxalic acid (AOOA). According to the results, the alperujo pectin extracted using ChCl from alcohol-insoluble residue (AIR) showed a higher yield (2.20–2.88% on the basis of dry weight of AIR) than using CA (0.65–1.22%) but lower than using AOOA (3.92–5.42%). For fruit pectin, the highest yield was obtained using CA (8.81–16%), followed by AOOA (5.4–6.63%), although for apple pectin, ChCl gave a similar yield (5.36%) to AOOA. The uronic acid contents in all ChCl pectins (45.9–70.6% dry basis AIR) were higher or similar to that of the other extracting agents (30.6–65.2%), although a lower level of neutral sugar side chains was detected, with a lower degree of branching and degree of methylation. The NMR and FT-IR spectroscopy of the pectin isolated using ChCl confirmed its slightly different structural composition with respect to CA and AOOA pectin. Therefore, depending on the source material and functionality, pectin isolated using ChCl could be an acid-free alternative to pectin production.