Introduction Beta‐cell autoantibodies are established markers of autoimmunity, which we compared between Ghanaian adults with or without diabetes, living in rural and urban Ghana and in three European cities. Methods In the multicenter cross‐sectional Research on Obesity and Diabetes among African Migrants (RODAM) study (N = 5898), we quantified autoantibodies against glutamic acid decarboxylase (GAD65Ab) by radioligand binding assay (RBA) and established cut‐offs for positivity by displacement analysis. In a subsample, we performed RBA for zinc transporter‐8 autoantibodies (ZnT8Ab). Associations of environmental, sociodemographic, and clinical factors with GAD65Ab were calculated. Results In this study population (age: 46.1 ± 11.9 years; female: 62%; Ghana‐rural: 1111; Ghana‐urban: 1455; Europe: 3332), 9.2% had diabetes with adult‐onset. GAD65Ab concentrations were the highest in Ghana‐rural (32.4; 10.8‐71.3 U/mL), followed by Ghana‐urban (26.0; 12.3‐49.1 U/mL) and Europe (11.9; 3.0‐22.8 U/mL) with no differences between European cities. These distributions were similar for ZnT8Ab. Current fever, history of fever, and higher concentrations of liver enzymes marginally explained site‐specific GAD65Ab concentrations. GAD65Ab positivity was as frequent in diabetes as in nondiabetes (5.4% vs 6.1%; P = .25). This was also true for ZnT8Ab positivity. Conclusion Geographic location determines the occurrence of GAD65Ab and ZnT8Ab more than the diabetes status. Beta‐cell autoimmunity may not be feasible to differentiate diabetes subgroups in this population. Among 5898 Ghanaian adults living in rural Ghana, urban Ghana, and three European cities, GAD65Ab was strongly determined by the environment. Thus, GAD65Ab may not differentiate autoimmune subgroups of adult‐onset diabetes.