In March 2021, Emergency Intake Sites (EIS) were created to address capacity shortfalls during a surge of Unaccompanied Children at the Mexico-United States land border. The COVID-19 Zone Plan (ZP) was developed to decrease COVID-19 transmission. COVID-19 cumulative percent (%) positivity was analyzed to evaluate the impact of the ZP, venue type and bed capacity across EIS from April 1–May 31, 2021. Results: Of 11 EIS sites analyzed, 54% implemented the recommended ZP. The overall % positivity was 2.47% (95% CI 2.39–2.55). The % positivity at EIS with the ZP, 1.83% (95% CI 1.71–1.95), was lower than that at EIS without the ZP, 2.83%, ( 95% CI 2.72–2.93), and showed a lower 7-day moving average of % positivity. Conclusion: Results showed a possible effect of the ZP on % positivity when controlling for venue type and bed capacity in a specific EIS group comparison, indicating that all three variables could have had effect on % positivity. They also showed that smaller intake facilities may be recommendable during public health emergencies.