The present investigation reported that FYM application in different seasons influenced root, shoot, and seedling length, straw K, vigour index-I, nutrient uptake, grain, and stover yield of pearl millet significantly (P < 0.05) and followed the order: both seasons > kharif > rabi. Applying FYM in both seasons resulted in higher N, P, and K content in pearl millet grain (1.99%, 0.17%, and 0.37%, respectively) followed by kharif season application (1.93, 0.16, and 0.35%, respectively). Applying 15 t FYM ha−1 significantly increased the grain N (13.19%), P (63.16%), K (22.29%), protein (13.56%), stover N (32.76%), P (46.66%) and root length (29.83%) over FYM0. After 50 cropping cycles, continuous application of FYM15, FYM10, and FYM5 significantly improved vigour index-I by 52.85, 39.26, and 23.63% over no FYM, respectively. Applying 120 kg N ha−1 significantly increased N (6.38%), P (15.89%), and protein (6.03%) content, germination (5.91%), and vigour indexes (24.52 to 30.91%) of pearl millet grain over no fertilizer N. The treatment FYM15 × N120 increased the seedling length of pearl millet by 30.54 over N120 and 11.08% over FYM15 alone, respectively. Adding FYM either during both seasons or in the kharif season along with fertilizer N proved superior in improving the quality and yield of pearl millet.