The prevalence of tobacco use increases in times of stress; however, during the initial stage of the COVID-19 pandemic, tobacco use rates stayed the same in most populations. Previous work focused on the initial months of the pandemic, while this study examined the changes in tobacco use during a later peak period of the pandemic. We used data from 61,852 visits to the VA San Diego Healthcare System from November 2019 to February 2021, divided into pre-, early, and peak pandemic periods. Multinomial logistic regression was used to test whether the odds of being a daily or non-daily tobacco user varied over time, by demographic group, or with the presence of specific psychiatric diagnoses. Younger Veterans had a greater reduction in the prevalence of non-daily tobacco use between the early and peak periods, while older Veterans had a rise in daily use from pre- to the early pandemic, which returned to baseline during the peak. Individuals with substance use disorder and serious mental illness diagnoses were more likely to report tobacco use, but psychiatric diagnoses did not predict change over time. These findings demonstrate factors that potentially contribute to changes in tobacco use during a public health crisis and may help guide future targeted cessation efforts.