Background: During the first two waves of COVID-19, several physical restriction measurements were imposed in Belgium. Our aim was to explore the impact of these restriction measures on the number of tests and positivity rate of Chlamydia trachomatis (CT) /Neisseria gonorrhoeae (NG) before, during, and after the two lockdowns in Belgium. Methods: Chlamydia trachomatis/Neisseria gonorrhoeae molecular data of a Belgian STI clinic were extracted for 2019 and 2020, and both years were divided into four periods (pre-lockdown 1, lockdown 1, after lockdown 1, and lockdown 2). Weekly testing rates and positivity rate for both STIs were estimated, and mixed-effects logistic regression was used to explore statistical significant changes between both years, and the different periods were compared with the corresponding time period in 2019. The same analysis was done for pre-exposure prophylaxis(PrEP) users only. Results: No overall significant changes in positivity rate were found for either CT (8.0% in 2019 and 7.8% in 2020) or NG (4.5% in 2019 and 5.5% in 2020). Besides a significant drop in the number of CT/NG tests during lockdown 1 (decrease of 87%) and a subsequent increase in NG positivity rate ( p > 0.05), no changes in CT/NG positivity rate were found in the other periods. The highest positivity rate for either CT or NG was found in lockdown 2 (15.1% vs 12.4% in 2019). The number of CT/NG tests in lockdown 2 was still 25% lower than 2019 levels. Subanalysis of only PrEP users revealed the same trend; however, the number of CT/NG tests in lockdown 2 was exactly the same as in 2019. Conclusion: Despite a significant decline in absolute CT or NG cases in lockdown 1, which was most likely a consequence of both physical distancing and reduced testing, CT/NG testing and positivity rates returned to pre-corona levels in lockdown 2, which may depict physical distancing fatigue.