Landraces are a valuable source of genetic variability for breeders to develop high-yielding lentil varieties. Apart from productivity, simultaneous breeding for lentil seed nutritional quality is of paramount importance for wider lentil consumption. This work examined the indirect effect of single plant selection for high yield on important seed quality traits within three Greek lentil landraces ("Elassona" (EL), "Lefkada" (L), and "Evros" (EV)). The breeding methodology applied was proved to help either maintain or improve such characteristics in the high-yielding second-cycle lines (SLs) selected. Compared to the parental landrace "Elassona", the high-yielding lines showed increased crude fiber by 30-110%; the line 2-SL-EL-6 had higher starch content by 3.9% and reduced cooking time by 6.67 min, while the 2-SL-EL-10 line had higher crude fiber by 73%. In the case of "Lefkada", the high-yielding lines selected maintained the protein content present in the parental landrace, apart from the 2-SL-L-1 where a decrease by 5% was recorded; however, most of them showed increased crude fiber (5.59-7.52%) in comparison with the parental landrace (4.65%). Finally, in relation to the "Evros" parental landrace, the 2-SL-EV-3 and 2-SL-EV-4 showed higher crude fiber and reduced cooking time. This study provides evidence that proper management of genetic variability could improve productivity without compromising or sometimes improving some seed quality traits.