After Maihar, Banerjee embarked on a concert career that was to take him to all corners of the world and last right up to his death. All through his life he kept taking lessons from Allauddin and his children, Ali Akbar and Annapurna Devi. Perhaps reflecting his early upbringing, he always remained a humble musician, and was content with much less limelight than a player of his stature could have vied for. For him, music-making was a spiritual rather than a worldly path. Even so, in 1968, he was decorated with the Padma Shri and posthumously received also the Padma Bhushan; at the time of his death by heart attack, he was a faculty member at the Ali Akbar College of Music in Calcutta. Nikhil Banerjee disliked teaching, and hence does not have any significant students. There are a few sitar players who are presently performing around the world who claim to be his students or disciples; they are not 'disciples' in the true sense. According to many sources close to Banerjee, he might give a lesson here or there to a dedicated student, but that was all. And considering the rigors of the guru-shishiya (master-disciple) relationship, one cannot say that Banerjee had any 'students'. Although he recorded extensively, the studio environment made Banerjee nervous. Not so the concert hall; his live albums, many of which were brought out around the turn of the 21st Century by Raga Records in New York, are widely considered to be the finest documents of his playing. Today, he is regarded as one of the greatest traditional sitarists of the 20th century.

His interpretation of ragas was usually traditional although he would some times take liberties with the raga in a moment of inspiration. Some people say he created a raga Manomanjari of his own, mixing ideas from Kalavati and Marwa, while other attribute it to Allaudin Khan.