Abstract Background We examined how the COVID-19 pandemic influenced influenza vaccination, healthcare engagement, and patient satisfaction. Methods We retrospectively analyzed influenza vaccination records and patient experience surveys of adult primary care patients in southeastern Minnesota during two 3-year phases: Prepandemic (1 January 2017–28 February 2020) and Pandemic-Plus (1 March 2020–31 December 2023). Vaccination status was defined as “always vaccinated” (AV), “never vaccinated” (NV), or “intermittently vaccinated” (IV) for seasonal influenza. Results During the Pandemic-Plus phase, 7.0% (n = 3556) of the Prepandemic AV and 48.7% (n = 16 710) of the Prepandemic IV patients never received another influenza vaccine. Compared to AV, IV and NV patients were more likely to reside in areas with greater socioeconomic deprivation (odds ratio [OR], 1.58 [95% confidence interval {CI}, 1.53–1.62] and 1.99 [1.94–2.05], respectively), have a high school education or less (2.86 [2.74–2.98] and 3.38 [3.23–3.53]), and report healthcare disengagement (1.59 [1.55–1.64] and 4.21 [4.09–4.33]). After adjusting for Area Deprivation Index and medical comorbidities, healthcare disengagement increased among the NV versus AV between phases (3.33 [3.24–3.41] and 4.23 [4.10–4.35]). In a subgroup analysis those with severe comorbidities were less likely AV (NV vs AV: 1.21 [1.14–1.27]) and more dissatisfied with care (NV vs AV: 1.25 [1.18–1.33]). Conclusions The COVID-19 pandemic altered vaccination behaviors and healthcare satisfaction, especially among those at high risk of developing influenza-related complications. Medical providers and public health officials should be aware of factors associated with vaccine refusal to better target interventions.