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Computer workers’ sedentary work, together with less active lifestyles, aggravated by the COVID-19 pandemic, represents a high risk for many chronic diseases, leading to a decrease in health-related quality of life (QoL). Workplace exercises consist of a set of physical exercises, implemented during work breaks, that have multiple benefits for workers’ health. Aim: To assess the impact of online workplace exercises on computer workers’ perception of quality of life. Methods: Quasi-experimental study with two groups: a control group (n = 26) and an intervention group (n = 13). The inclusion criteria were that participants must be aged between 18 and 65 years old and the exclusion criteria included diagnosis of non-work-related medical conditions. The interventions consisted of workplace exercises, which were applied for 17 consecutive weeks, each session lasting 15 min, three times a week. The exercise programme, performed online and guided by a physiotherapist, consisted of mobility exercises, flexibility and strength exercises, with the help of a TheraBand® for elastic resistance. The control group were not subjected to any intervention. A socio-demographic questionnaire and the Health Survey Questionnaire (SF-36v2) were used in two assessment stages (M0—baseline and M1—final of intervention). A mixed ANOVA with interaction time*group was used to evaluate the effect of the exercise programme. Results: A good perception of the QoL was obtained in both stages. The exercise programme had a positive effect in the domains of Pain (ptime*group = 0.012, η2p = 0.158), Physical Function (ptime*group = 0.078, η2p = 0.082), Physical Performance (ptime*group = 0.052, η2p = 0.098), and Emotional Performance (ptime*group = 0.128, η2p = 0.061). Conclusion: After 17 weeks of workplace exercises, it became clear that the intervention group positively increased their QoL perception, with this improvement being significant in the Pain domain, which resulted in an improvement in their health condition. Therefore, further studies are needed to determine the optimal exercise for CWs, with detailed exercise types, different intensities and focused on various health conditions.