Bush tea (Athrixia phylicoides DC.) is an herbal beverage and medicinal plant indigenous to South Africa. This study evaluated the effects of micronutrients on bush tea quality. Treatments consisted of single applications of zinc (Zn), copper (Cu), boron (Bo), iron (Fe), and magnesium (Mg) at three levels (50, 100, and 150 mL/L) and a combination of all micronutrients. A control treatment with no spray was also included. Tea samples were analyzed using head space solid phase microextraction gas chromatography linked to mass spectrometry (HS-SPME-GC-MS). A significant change in the metabolite profile of bush tea was noted. Five major compounds were identified (>80% identification probability) namely alpha-pinene, beta-pinene, myrcene, beta-caryophyllene, and caryophyllene oxide. A linear relationship between percentage leaf tissues and treatment levels of micronutrients in bush tea was also observed. The liquid chromatography linked to mass spectrometry (LC–MS) showed no significant qualitative difference between the control and the micronutrient treatments. There were significant quantitative differences between the control and treatments applied at 50 and 100 mL/L and the combination (B + Zn + Fe + Cu + Mg) applied at 10 and 20 mL/L. The application of micronutrients did have an influence on the metabolite quantities as has been reported with most secondary metabolite fluctuations caused by plant–environment interactions. Altering the micronutrient application may be a possible solution in achieving commercial agricultural production of this medicinal beverage.