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Understanding genotype by environment interaction (GEI) represents a challenge in Kersting's groundnut [Macrotyloma geocarpum (Harms) Maréchal and Baudet] breeding for selecting high‐performing and stable lines across environments. Here, we investigated GEI and stability in Kersting's groundnut using factor analytic (FA) based linear mixed models and environmental covariates. A total of 375 accessions were evaluated across 3 years (2017, 2018, and 2019) and two locations (Sékou and Savè) in Benin, generating five environments (E1, E2, E3, E4, and E5). The traits measured included days to 50% flowering (DFF), grain yield (YLD), and 100‐seed weight (HSW). The study generated multi‐environment values for grain yield and its components in Kersting's groundnut. The genetic correlations between pairs of environments ranged from −0.71 to 0.99. The genetic correlations between YLD and HSW indicated positive and moderate to high correlations in all environments. The FA analysis revealed that FA2 structure accounted for 93.9% of the genetic variability in DFF with factor 1 accounting for more than 90% of the environments variations. Two factors explained 87% of the genetic variance in grain yield, and 70% of the environments variability were clustered by factor 1. For HSW, two factors explained 85% of the genetic variance of the environments, and factor 1 accounted for 72.7%. Combining environmental covariates to FA models revealed that precipitation, temperature, and growth cycle duration were highly correlated to the environmental loadings of factor 1. Relative humidity and solar radiation showed moderate to high correlations with factor 2 loadings. Those covariates explained the high GEI among environments clustered by a given factor. Precipitations and temperatures affected the variations in grain yield. Finally, based on latent regression analysis, the accessions AF202, AF221, AF223, AF225, and AF256 were identified as accessions combining best performance for grain yield, early flowering, and 100‐seed weight, showing adaptability across environments and stability to some environments. Core Ideas: In plant breeding, understanding the genotype by environment interaction (GEI) represents a challenge for selecting high‐performing and stable lines across environments, especially for development of climate‐smart cultivars of Kersting's groundnut (Macrotyloma geocarpum).Multiplicative factor analytic (FA) structures have been proposed as a more parsimonious approach dealing with unbalanced data and allowing analysis of main factors affecting GEI.Latent regression plots of superior genotypes across environments and FA structures are efficient to infer about GEI, adaptability, and stability of Kersting's groundnut accessions.The environmental loadings of FA models can be correlated to climatic covariates to examine trends in the genotypes' performance across environments according to environmental conditions. [ABSTRACT FROM AUTHOR]