Background Due to the COVID-19 pandemic, emergency situation for social distancing was implemented in many countries, including Estonia. For most office workers, the lockdown caused a sudden shift from working at the office to working from home. The lockdown offered an opportunity to investigate how working from home affects musculoskeletal pain (MSP), physical activity (PA), work environment factors and their inbetween relationships among office workers. Objective The aim of this study was to evaluate the COVID-19 lockdown caused changes in MSP, PA, workplace properties and their inbetween relationships among office workers. Methods The study was conducted as an online form, which consisted of Baecke Physical Activity Questionnaire, modified NORDIC Musculoskeletal Questionnaire and questions about work environment. The questionnaires were doubled: one for describing the situation during the lockdown, second for describing retrospectively about 3 months before the lockdown. Total of 161 office workers (64,6% female) participated with the mean age of 38,17±9,52 years. Results We did not find any significant differences in the prevalence of MSP or between the mean number of body regions suffering from MSP before and during the lockdown. There was a significant (p<0,001, Cohen’s d=0,26) reduction in total PA, a significant (p<0,001, Cohen’s d=0,5) increase in work-related PA and a significant (p<0,001, Cohen’s d=0,42) decrease in sport-related PA during the lockdown. We found a significant drop in both workplace comfort rating (p<0,05, Cohen’s d=0,27) and workplace ergonomics rating (p<0,001, Cohen’s d=1). We recorded a significant negative correlation (r=-0,2059, p<0,01) between the change in self-reported sport-related PA and the change in number of body regions with MSP. We recorded a significant negative correlation between the number of body regions with an onset of MSP during the lockdown with both workplace comfort score (r=-0.262, p<0,001) and workplace ergonomics score (r=-0,2305, p<0,01). Conclusion Maintaining habitual physical activity levels and preparing a more comfortable and ergonomic workspace can play an important role in healthier transition to working from home.