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Lentil is an important legume crop for human and animal dietary needs due to its high nutritional value. The effect of genotype and growing environment was studied on seed yield (SY), crude protein (CP) and mineral nutrients (macro and micronutrients) of five lentil genotypes grown at four diverse locations for two consecutive years under organic and conventional farming. The location within each year was considered as a separate environment (E). Data were subjected to over environment two-way analysis of variance, while a genotype (G) plus genotype × environment (GGE) biplot analysis was performed. Our results indicated the E as the main source of variation (62.3–99.8%) for SY, CP and macronutrients for both farming systems, while for micronutrients it was either the E or the G × E interaction. Different environments were identified as ideal for the parameters studied: E6 (Larissa/Central Greece/2020) produced the higher CP values (organic: 32.0%, conventional: 27.5%) and showed the highest discriminating ability that was attributed to the lowest precipitation during the crucial period of pod filling. E7 (Thessaloniki/Central Macedonia/2020) and E8 (Orestiada/Thrace/2020) had fertile soils and ample soil moisture and were the most discriminating for high micronutrient content under both farming systems. Location Orestiada showed the highest SY for both organic (1.87–2.28 t ha−1) and conventional farming (1.56–2.89 t ha−1) regardless the year of cultivation and is proposed as an ideal location for lentil cultivation or for breeding for high SY. Genotypes explained a low percentage of the total variability; however, two promising genotypes were identified. Cultivar “Samos” demonstrated a wide adaptation capacity exhibiting stable and high SY under both organic and conventional farming, while the red lentil population “03-24L” showed very high level of seed CP, Fe and Mn contents regardless E or farming system. This genetic material could be further exploited as parental material aiming to develop lentil varieties that could be utilized as “functional” food or consist of a significant feed ingredient.