The aim of the study is to examine the changes in the burden of secondary health conditions and their risk factors among newly injured individuals with spinal cord injury after discharge from inpatient rehabilitation to community living. This is a prospective cohort study. Among 280 included persons, the majority were men with traumatic spinal cord injury and paraplegia. The most common secondary health conditions at discharge from rehabilitation and in the community setting were pain (60.8% vs. 75.9%), urinary tract infections (27.8% vs. 47.6%), and pressure sores (9.9% vs. 27.5%). There was also a significant increase in reported heart disease (9.3% vs. 14.8%) and diabetes (0% vs. 4.2%). The odds of experiencing pain, pressure sores, depression and urinary tract infections increased after discharge from rehabilitation, whereas the odds of respiratory problems decreased significantly during the observation period. Factors such as sex, injury severity, activity limitations, and duration of follow-up were identified as potential risk factors influencing secondary health condition occurrence. Our study emphasizes a significant rise in secondary health conditions after the transition to community living. Future research should prioritize development of targeted intervention programs tailored to address the unique needs of affected individuals at this pivotal stage in the continuum of spinal cord injury care.