The objective of this study was to investigate the influence of nanoclay incorporation procedure on the mechanical and water vapor barrier properties of starch/nanoclay composite films. Cassava starch films were prepared with (nanocomposite) and without nanoclay (control) in two steps: firstly the production of extruded pellets and secondly thermo-pressing. The nanocomposite films were prepared via two different methods: in D samples the nanoclay was dispersed in glycerol and subsequently incorporated into the starch; and in ND samples all ingredients were added in a single step before the extrusion. All the composite-films were prepared with cassava starch using 0.25g of glycerol/g of starch and 0.03g of nanoclay/g of starch. Control samples showed VA-type crystallinity induced by the manufacturing process and the nanocomposites presented a semicrystalline and intercalated structure. The nanoclay improved the water vapor barrier properties of the starch film and this effect was more pronounced in D samples, where the water vapor permeability (Kw) was 60% lower than that of the control samples. The Kw reduction was associated with decreases in the effective diffusion coefficient (approximately 61%) and in the coefficient of solubility (approximately 22–32%). On the other hand, the incorporation of nanoclay increased the tensile strength and the rigidity of the films and this effect was more significant when the nanoclay was dispersed in glycerol. Thus, the incorporation of nanoclay into starch-based films is a promising way to manufacture films with better mechanical and water vapor barrier properties.