The emergence of COVID-19 so far and in the immediate future has brought significant uncertainties that negatively impact institutions and individuals in developing and planning their activities worldwide. The uncertainty of the effectiveness of vaccines has forced the authorities to adopt different protocols, the most relevant of which is the isolation of people through quarantine to avoid contagion, drastically affecting our way of life. For this reason, it is crucial to evaluate the effectiveness of quarantines. In this paper, we analyze the spread of the disease in Chile according to the quarantines decreed by the sanitary authority. An inferential study is used to estimate the trend changes in COVID-19 cases and their basic and instantaneous reproduction numbers, which allows us to evaluate the decreed measures and establish vaccination policies. According to the data obtained until 03 March 2021 of confirmed COVID-19 cases disaggregated at a regional level in Chile, we observe a heterogeneous spread in most Chilean regions. When incorporating the dynamic quarantines decreed, effectiveness is detected in most regions, except in a few of them. Our results indicate that we are unable to identify the measures in the step-by-step protocols partly responsible for non-compliance with quarantines. However, our specific findings that can be extrapolated to daily practice and enlighten the ways of other countries are as follows. On the one hand, a measure that has been effective in curbing the spread of the disease is the strict early quarantine as detected in some Chilean regions. Therefore, indexes are needed to measure the mobility of citizens. On the other hand, as time passes without stopping infections, quarantines lose effectiveness even if the estimated instantaneous reproduction number is negligible and stable. In addition, other factors can cause this number to not be within the expected ranges, which must be further studied. Also, we have estimated the basic reproduction number whose value confirms the suitability of the pandemic declaration.