This study develops and validates a multi-scale modeling framework to estimate biogas production from the anaerobic co-digestion (AcoD) of cattle manure and tomato crop waste (Solanum lycopersicum L.), an abundant and underutilized agricultural residue in Mexico. The modeling approach integrates three complementary mathematical models (Volume Averaging, Laplace Domain, and Modified Gompertz equation) which were fitted to experimental data previously reported in the literature. These data were obtained from batch bioreactors experiments conducted under different operational conditions (20% and 50% substrate on a dry basis, and pH 6.8 and 7.5). The models exhibited a strong fit (R²: 0.84 – 0.97; RMSE = 0.10 – 1.10), supporting their suitability for describing both kinetic and transport phenomena. The Volume Averaging method enabled the estimation of transport parameters, including diffusion coefficients on the order of 1.6×10−6 m²/d, along with key reaction parameters. The Laplace Domain approach facilitated the dynamic characterization of the system through transfer functions, while the Modified Gompertz equation accurately captured biogas production kinetics. The results indicate that operating at 50% substrate concentration with pH control reduced the characteristic production time to approximately 30 days, which is less than half the time required for the 20% substrate condition (60-66 days)  and achieved methane contents of up to 41%, approaching the established threshold for biogas as biofuel (45%), with V50a showing the highest methane fraction. The estimated kinetic and transport coefficients suggest a clear metabolic adaptation of the microbial consortia under optimal conditions. Overall, this integrated framework demonstrated its potential for the design and scale-up of AcoD systems, providing a link between physicochemical fundamentals and practical application in agricultural regions with high organic waste generation.