The aim of this study was to obtain cellulose and cellulose nanoparticles (CNP) from garlic and agave wastes, as well as elucidating its structure at different scales using microscopy and spectroscopy techniques. Cellulose is isolated by using a sequential extractive process and monitored by CLSM and SEM, while CNP are produced in a high-energy planetary mill. FTIR and XRD confirmed the presence of cellulose type I and CI and Dhkl was used to evaluate the size of CNP. The corresponding crystalline structure, d-spacing and angles obtained from crystalline regions of CNP were estimated by TEM and computational simulation. It is shown that the triclinic phase is predominant in G, and a monoclinic conformation in CNP for A. The novelty of this contribution is to demonstrate that the crystalline structure of CNP, extracted from different agro-food wastes, depends on its initial microstructural arrangement (laminar or fibrillar).