To establish a “green” biorefinery extraction of apple pomace pectin, a sequential pretreatment with three natural deep eutectic solvents (NADES, choline chloride (CC): glycerol (G); CC: lactic acid (LA); potassium carbonate (K): G) was used prior to hot water extraction. A synergistic effect of CC:G and CC:LA pretreatments was observed and led to the highest recovery of pectin. The sequential NADES/water extraction process also provided a mean to tailor pectin main structure. It was explained as resulting from ion exchange and individual NADES components effects. The 13C solid state NMR T1ρH and THH parameters indicated a reorganization of cellulose in the residues following extraction of pectin, notably after alkaline K:G pretreatment/water extraction. Hence, sequential NADES pretreatments/water extraction represents a “green” alternative to mild mineral acid to extract pectin and to tailor its main structures, while the residual pomace can be further sources of valuable compounds and polymers.