Background In the UK, there have been multiple waves of coronavirus disease 2019 (COVID-19), with a five-tier alert system created to describe the transmission rate and appropriate restrictions. While acute mortality decreased, there continues to be significant morbidity, with individuals suffering persistent, life-restricting symptoms for months-to-years afterwards. A remote rehabilitation tool was created at the Defence Medical Rehabilitation Centre (DMRC) Stanford Hall to assess post-COVID-19 symptoms and their impact on the UK Military. This study aims to understand changes in post-COVID-19 syndrome between wave one and wave two, identify interactions between alert level and symptoms, and investigate any predictive nature of acute symptoms for post-acute symptomology in a young, physically-active population. Methods Cross-sectional study of 458 consecutive remote rehabilitation assessments performed at DMRC Stanford Hall between 2/4/2020 and 29/7/2021. Consultations were coded, anonymised, and statistical analysis was performed to determine associations between acute and post-acute symptoms, and between symptoms, alert level, and wave. Results 435 assessments were eligible; 174 in wave one and 261 in wave two. Post-COVID-19 syndrome prevalence reduced from 43% to 2% between the waves. Acutely, widespread pain was more prevalent in wave two (P<0.001). Post-acutely, there was increased anxiety (p=0.10) in wave one and increased sleep disturbance (p<0.001), memory/concentration issues (p<0.001), and shortness of breath/cough (p=0.017) in wave two. Increasing alert level was associated with increased post-acute symptom prevalence (p=0.046), with sleep disturbance increasing at higher alert level (p=0.016). Acute symptoms, including fatigue, sleep disturbance and myalgia, were associated with multiple post-acute symptoms. Conclusions This study reports the overall prevalence and symptom burden in the UK Military in the first two waves of COVID-19. By reporting differences in COVID-19 in different waves and alert level, this study highlights the importance of careful assessment and contextual understanding of acute and post-acute illness for individual management plans.