Background: Pulmonary function can be impaired as a long-term consequence of SARS-CoV-2 infection. The aim of this study was to evaluate the effect of SARS-CoV-2 infection on pulmonary function, exercise tolerance, and muscle strength in healthy middle-aged military outpatients according during the period of infection. Methods: A cross-sectional study was carried out from March 2020 to November 2022 at the Military Hospital “Celio” (Rome, Italy). If someone had a diagnosis of SARS-CoV-2 infection certified by molecular nasal swab and if they performed pulmonary function tests, diffusion of carbon monoxide (DL’co), a six Minute Walk Test (6MWT), a Handgrip (HG) Test, and a One Minute Sit to Stand Test (1′STST). The included subjects were divided into two groups, A and B, according to the period of infection: A) from March 2020 to August 2021 and B) from September 2021 to October 2022. Results: One hundred fifty-three subjects were included in the study: 79 in Group A and 74 in Group B. Although the values were within the normal range, Group A had smaller FVC, FEV1,and DL’co compared to Group B. Group A also walked a shorter distance at the 6MWT and performed fewer repetitions in the 1′STS test compared to Group B. In both groups, the DL’co (%predicted) correlated with the 6MWT distance (R2= 0.107,p< 0.001), the number of repetitions of the 1′STST (R2= 0.086,p= 0.001), and the strength at the HG test (R2= 0.08,p< 0.001). Conclusions: This study shows that the SARS-CoV-2 infection in healthy middle-aged military outpatients was more severe in the first waves than in the later ones and that, in healthy and physically fit individuals, even a marginal reduction in resting respiratory test values can have a major impact on exercise tolerance and muscles strength. Moreover, it shows that those infected more recently had symptoms related to the upper respiratory tract infection compared to those of the first waves.