Degenerative joint disease (DJD) is one of the most common pathological conditions identified in the archaeological record and remains a health problem in modern populations. This study aimed to evaluate DJD of the vertebral column in a sample from a Chalcolithic collective burial at El Mirador cave (Sierra de Atapuerca, Spain) dated to 4,880–4,390 years cal. BP. Most of the human remains recovered were commingled and are in a good state of preservation. Traditionally, far too little attention has been paid to skeletal remains from secondary contexts. Bearing in mind the limitations inherent to this type of study, in this work, we applied an adapted methodology to examine the degree of vertebral degeneration considering the skeletal changes associated with DJD (i.e., osteophyte formation, porosity, lipping and/or eburnation). All data were evaluated at the 0.05 level using the chi‐squared statistic, and comparisons were made between age groups and between the spine regions. Our results showed a higher prevalence of DJD in the lumbar region, although eburnation was the least observed marker in the sample. Additionally, significant differences were found between age groups, with a greater manifestation of DJD in vertebral elements associated with the adult group. These results are consistent with those of other studies and are based on the hypothesis that DJD is highly correlated with age. Overall, the degree of vertebral degeneration is low, but taken together, these results suggest that some individuals from El Mirador cave may have suffered from DJD. Furthermore, the methodology proposed has demonstrated that valuable information can be obtained from commingled skeletal assemblages.