The enteric methane conversion factor (Ym) is an important country-specific value for the provision of precise enteric methane emissions inventory reports. The objectives of this meta-analysis were to develop and evaluate the empirical Ym models for the national level and the farm level for tropical developing countries according to the IPCC’s categorization. We used datasets derived from 18 in vivo feeding experiments from 1999 to 2015 of Zebu beef cattle breeds fed low-quality crop residues and by-products. We found that the observed Ym value was 8.2% gross energy (GE) intake (~120 g methane emission head−1 day−1) and ranged from 4.8% to 13.7% GE intake. The IPCC default model (tier 2, Ym = 6.5% ± 1.0% GE intake) underestimated the Ym values by up to 26.1% compared with its refinement of 8.4% ± 0.4% GE intake for the national-level estimate. Both the IPCC default model and the refined model performed worse in predicting Ym trends at the farm level (root mean square prediction error [MSPE] = 15.1%–23.1%, concordance correlation coefficient [CCC] = 0.16–0.18, R2 = 0.32). Seven of the extant Ym models based on a linear regression approach also showed inaccurately estimated Ym values (root MSPE = 16.2%–36.0%, CCC = 0.02–0.27, R2 < 0.37). However, one of the developed models, which related to the complexity of the energy use efficiencies of the diet consumed to Ym, showed adequate accuracy at the farm level (root MSPE = 9.1%, CCC = 0.75, R2 = o.67). Our results thus suggest a new Ym model and future challenges for estimating Zebu beef cattle production in tropical developing countries.