The aim of this observational study was to investigate the level and association of physical activity and selected chronic diseases in functionally independent LTC residents after prolonged physical and social isolation during COVID-19 in Croatia. Adhering to the inclusion criteria, 180 functionally independent residents were included in the study. Assessment of physical activity was carried out by 7-day motor monitoring. Prolonged physical and social isolation negatively affected the achieved level of physical activity of LTC residents ($\overline{\mathrm{x}}$ = 5058.74). Major depressive disorder resulted in significantly lower residents’ physical activity scores, demonstrating a shrinking effect ranging from 0.42 to 0.45. A significant negative impact on the residents’ physical activity was also found in the presence of osteoarthritis and iron deficiency anemia, where a downward effect was present in the range from 0.66–0.72 and 0.64 to 0.66. The presence of comorbidities has a significant negative impact on the residents’ physical activity, where a downward effect is present in the range from 0.91–0.92.