Will antibiotics continue to work after you stop taking them? Yes, antibiotics continue their antibacterial effects after your last dose. Some will last in the body longer than others. While doxycycline may take several days to clear, amoxicillin is excreted from the body more quickly.
If you stop treatment before the antibiotic cycle is over, the remaining bacteria can continue to multiply. If these bacteria become resistant to the antibiotics, they can potentially do even more harm. It may take longer for you to recover from your illness, and your physician may have to prescribe more medication.
After an antibiotic course, recovery of the gut microbiome can take some time. In general, after short-term antibiotic use (between five and ten days), studies have observed it can take at least one to two months for most bacterial groups to recover to pre-antibiotic levels2,3,13–16.
Each time you take an antibiotic, bacteria are killed. Sometimes, bacteria causing infections are already resistant to prescribed antibiotics. Bacteria may also become resistant during treatment of an infection. Resistant bacteria do not respond to the antibiotics and continue to cause infection.