The influence of cellulose crystallinity on mechanical properties of cellulose nano-fibrils (CNF) was investigated. Degree of crystallinity (DoC) was modified using liquid anhydrous ammonia. Such treatment changes crystal allomorph from cellulose I to cellulose III, a change which was reversed by subsequent boiling in water. DoC was measured using solid state nuclear magnetic resonance (NMR). Crystalline index (CI) was also measured using wide angle X-ray scattering (WAXS). Cotton linters were used as the raw material. The cotton linter was ammonia treated prior to fibrillation. Reduced DoC is seen to associate with an increased yield point and decreased Young modulus. Young modulus is here defined as the maximal slope of the stress–strain curves. The association between DoC and Young modulus or DoC and yield point are both statistically significant. We cannot conclude there has been an effect on strainability. While mechanical properties were affected, we found no indication that ammonia treatment affected degree of fibrillation. CNF was also studied in air and liquid using atomic force microscopy (AFM). Swelling of the nanofibers was observed, with a mean diameter increase of 48.9%.