In 2020, preventive measures were implemented to mitigate the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 600-700 recruits arriving weekly in the Army’s largest basic combat training (BCT) facility. At the time of this study, public health officials relied on non-pharmaceutical interventions (NPI) as a main strategy to contain and mitigate the disease. In order to maintain medical readiness and operational mission, trainees were sorted into companies and platoons (or “cocoons”) at arrival, tested, quarantined for 14 days with daily temperature and respiratory symptom monitoring and retested before release into larger groups for training where symptomatic testing was conducted. This entry phase (called “yellow phase”) involved didactic curriculum such that continual training will occur without disruption of operational tempo plus containing any risk for close contacts with other cocoons. NPI measures such as masking, hand washing, and social distancing, were maintained throughout the “yellow phase” quarantine and throughout the remainder of the training cycle. We assessed for SARS-CoV-2 transmission in the quarantine milieu. Nasopharyngeal (NP) swabs were collected at arrival and at the end of quarantine and blood specimens at both timepoints and at the end of BCT. Epidemiological characteristics were analyzed for transmission clusters identified from whole-genome sequencing of NP samples. Among 1403 trainees enrolled from 25 August to 7 October 2020, epidemiological analysis identified three transmission clusters (n = 20 SARS-CoV-2 genomes) during quarantine, which spanned five different cocoons. However, SARS-CoV-2 incidence decreased from 2.7% during quarantine to 1.5% at the end of BCT; prevalence at arrival was 3.3%. These findings suggest layered SARS-CoV-2 mitigation measures implemented during quarantine minimized the risk of further transmission in BCT.