In the present work two agricultural residues (apple tree pruning and pea stalks) were studied as sources of nanocellulose. Different pretreatments that might be used in a biorefinery were applied to these lignocellulosic materials: autohydrolysis, organosolv (acetosolv) and alkaline pretreatments. After conventional bleaching, the resulting cellulosic fractions were submitted to a classical acid hydrolysis for nanocellulose crystal (NCC) production. The results showed that after applying different pretreatments, the resulting NCCs had different lengths (from 300 to 676 nm), surface charges (from 17 to 98 μmol acid groups/g NCC), purity (from 0.3 to 11.6% w/w of inorganics), crystallinity indexes and even allomorphism. These results highlighted the importance that cellulose source and particularly the applied pretreatments have on nanocrystal properties and suggest how biorefining pathways for lignocellulosic materials could customize such NCC features as surface reactivity or suitability for chemical modification.