Graphical abstract depicting the simultaneous effect of increased in-plane ordering and N doping concentration and distribution, on the intercalation capacity of N -doped carbon microspheres (NDCMS). The highest interaction capacity is depicted by NDCMS-600 (depicting lower inplane order and high pyrrolic content), followed by NDCMS-800 (depicting longer inplane order and but lower pyrrolic N. While as lowest intercalation capacity is depicted by NDCMS-1000 which has structural features equivalent to NDCMS-600 but the lowest nitrogen concentration with negligible pyrrolic N in its structure. • The rare disorder–order-disorder structural transition and its correlation with electrochemical storage is the novel element in this work. • The simultaneous effect of hard carbon structuring and N doping (percentage and structuring) on Na storage through intercalation is observed herein. • The low-temperature carbonization proceeding with high in-plane graphitization, with high I G /I D ratios, is a unique observation presented here. • The possible influence of interplay between the N doping distribution and corresponding structural modification on the electrochemical behavior is highlighted. The inclusion of heteroatom in the hard carbon structure influences the crystal structure and electrochemical behavior to a considerable degree. Herein, we probe N- doped hard carbon series synthesized from a dairy waste at three synthesis temperatures of 600 °C, 800 °C and 1000 °C. The N -doped carbon microspheres (NDCMS) thus achieved, depict varying structural features that have been observed to hugely influence their electrochemical behavior. The rare disorder–order-disorder structural transition in the in-plane order has been observed among the NDCMS samples with NDCMS-800 depicting a high I G /I D ratio of 2.7 while NDCMS-600 and NDCMS-1000 depicted I G /I D ratio of 1.4 and 1.0 respectively. The N doping concentration varied as 4.1, 3.9, and 2.7 atom % for NDCMS-600, NDCMS-800, and NDCMS-1000, respectively. The doped N existed as pyridinic, pyrrolic, graphitic, and pyridinic oxide functionalities with NDCMS-600 possessing the 23.8 % pyrrolic N and 12.8 % graphitic N content. The N distribution changes to 8.8 % pyrrolic and 20.5 % graphitic in NDCMS-800 while the pyrrolic N content settles to 1.6 atom % and graphitic content increasing to 29.8% in NDCMS-1000. The electrochemical behavior, typically the intercalation exhibited a strong dependence on the above structural features. The NDCMS-600 with short-range order and high pyrrolic N content depicted the highest intercalation capacity of 130 mAhg −1 (total observed capacity is 171 mAhg −1 ). The NDCMS-800 which depicts lower pyrrolic content and long-range in-plane order exhibited an intercalation capacity of 102 mAhg −1 (total observed capacity is 125 mAhg −1 ). The NDCMS-1000 with reduced in-plane order and least pyrrolic content exhibits the lowest intercalation capacity of 51 mAh g −1 (total observed capacity is 75 mAh g −1 ). The intercalation kinetics is also seen to be influenced by structural variations among the NDCMS samples with R ct of ∼ 539 Ω, 787 Ω, and 1037 Ω for NDCMS-600, NDCMS-800, and NDCMS-1000 respectively.