Antibiotics are non-biodegradable drugs that inhibit the expansion and growth of microorganisms. Especially with the prevalence of Covid-19, the consumption of antibiotics has increased. Therefore, the presence of most prescribed antibiotics from ß-lactams including amoxicillin and cephalexin were studied at two municipal WWTPs in Isfahan. The analytical method was to extract antibiotics from the aqueous phase and then detected them via HPLC/UV. Samples were collected from 2 WWTPs for 13 sampling periods over 2 months between February and March 2020 during the outbreak of Covid-19. In WWTP A, the average concentration of amoxicillin in influent, effluent, and its removal efficiency was 509.64 ± 161.97 µg/L, 352.96 ± 203.88 µg/L, 34.35 ± 31.38%, and the average concentration of cephalexin in influent, effluent, and its removal efficiency was 189.42 ± 176.06 µg/L, 32.6 ± 49.59µg/L, 78.75 ± 23.81%, respectively. In WWTP B, the average concentration of amoxicillin in influent, effluent, and its removal efficiency was 2134.82 ± 3031.53µg/L, 401.09 ± 205.86µg/L, and 54.82 ± 33.29%, respectively. Also, the average concentration of cephalexin in influent, effluent, and its removal efficiency was 183.69 ± 123.48 µg/L, 23.01 ± 40.71 µg/L, and 87.65 ± 21.76%, respectively. According to Mann–Whitney test results, the concentration of antibiotics in both WWTPs had significant differences (p-value < .05), and according to results from the Spearman test no correlation between removal efficiency of antibiotics with other principles wastewater parameters was observed.