Mitigation of climate change depends on accurate estimation and mapping of terrestrial carbon stocks, particularly in carbon dense tropical forests. Allometric equations can be used to robustly estimate biomass of tropical trees, but often require tree height, which is frequently unknown. Researchers and practitioners must, therefore, decide whether to directly measure a subset of tree heights to develop diameter : height (D:H) equations or rely on previously published generic equations. To date, studies comparing the two approaches have been spatially restricted and/or not randomly allocated across the landscape of interest, making the implications of deciding whether or not to measure tree heights difficult to determine. To address this issue, we use inventory data from a systematic-random forest inventory across Gabon (102 forest sites; 42,627 trees, including 7,036 height-measured trees). Using plot-specific models of D:H as a benchmark, we compare the performance of a suite of locally fitted and commonly used generic models (parameterized national, georegional, and pantropical equations) across a variety of scales, and assess which abiotic, anthropogenic, and topographical covariates contribute the most to bias in height estimation. We reveal marked spatial structure in the magnitude and direction of bias in tree height estimation using all generic models, due at least in part to soil type, which compounded to substantial error in site-level AGB estimates (of up to 38% or 150 Mg/ha). However, two generic pantropical models (Chave 2014; Feldpausch 2012) converged to within 2.5% of mean AGB at the landscape scale. Our results suggest that some (not all) pantropical equations can extrapolate AGB across large spatial scales with minimal bias in estimated mean AGB. However, extreme caution must be taken when interpreting the AGB estimates from generic models at the site-level as they fail to capture substantial spatial variation in D:H relationships, which could lead to dramatic under- or over-estimation of site-level carbon stocks. Validated allometric models derived at site- or soil-type-levels may be the best way to reduce such biases arising from landscape-level heterogeneity in D:H model fit in the Afrotropics.