Fluoride-substituted hydroxyapatite (FHA) can be used for biomaterial applications because it has biocompatible properties. FHA is formed by replacing flour ion (F−) with hydroxyl ion (OH−) from hydroxyapatite. This work aims to see the influence of changes in the form of acidity (pH) at the FHA synthesis process using microwave irradiation method. FHA nano-powder was synthesized using a titration of calcium hydroxide solution with diammonium hydrogen phosphate and ammonium fluoride, which will vary the level of fluoride at FHA by 0.9 and 1.3. Subsequently, HCl 1 M or NaOH 1 M to give a variation of pH value. X-ray diffraction (XRD), Fourier transform infrared (FTIR), scanning electron microscopy (SEM), and energy-dispersive X-ray (EDX) spectroscopy analysis techniques were utilized to evaluate the characteristic of synthesized FHA nano-powder. The XRD and FTIR results showed that the powder with pH under control conditions had several additional formed phases such as chlorapatite and carbonate. The value of crystallinity had the distinction of each powder in each pH, but only pH control had crystallinity values, such as tooth enamel. Using the Scherrer formula, the average crystallite size was found around 21-80 nm. SEM and EDX characterization results showed the Ca/P ratio formed was 1.34. The results showed that the addition of acid resulted in the formation of a new phase which dominated and revamped some crystal parameters. Therefore, the synthesis in these conditions is not recommended.