Changes in cytokinin (CK) profiles and their physiological implications in micropropagated Harpagophytum procumbens [(Burch.) DC. ex Meisn.] tissues in relation to shoot-tip necrosis (STN) and CK treatments were studied. Total CK content was quantified in benzyladenine (BA)-treated necrotic and normal plantlets and in plantlets treated with the CKs BA, meta-topolin (mT) and meta-topolin riboside (mTR) with and without the auxin indole-3-acetic acid (IAA). Generally necrotic shoots yielded more total CK compared to normal shoots. Cytokinin accumulation was higher at the basal section (basal > middle > top). Further analysis of the CKs based on structural and functional forms revealed excessive accumulation of 9-glucosides (deactivation products—toxic metabolites) and limited amounts of O-glucosides (storage forms—re-utilizable) in necrotic and BA-treated shoots compared to normal and topolin-treated cultures. The addition of IAA enhanced the formation of 9-glucosides in BA-treated cultures but reduced it in topolin-treated cultures. The symptom of STN could therefore be attributed to conversion of active cytokinins to other forms such as 9-glucosides which are neither active nor reversibly sequestrated to active forms. Literature shows that metabolites like 9-glucosides of BA have a detrimental effect in plant tissue culture.