The purposes of this research are to study the effect of different natural antimicrobial agents and to evaluate their functional groups inhibition reactivity on bacterial growth. The investigated antimicrobial agents were aloe vera powder and citric acid. The evaluation of antimicrobial activity was done by using agar well diffusion method. The bacteria used for the assessment were Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). The functional groups were investigated by Fourier Transform Infrared (FTIR) spectroscopy. Only the antimicrobial agent citric acid showed significant inhibition towards both bacteria growth. The diameter of inhibition zone for S. aureus was larger compared to E. coli. The FTIR spectra showed the presence of functional groups only in citric acid agent. Citric acid has potential to be used as an alternative antimicrobial agent in the many applications including biomedical.