Biomarkers have been postulated as essential variables to measure the effects of exercise on the human body. To investigate the relationship between physical fitness (PF) and blood biomarkers that are associated with disease risk in Spanish older adults, four hundred and twenty-nine adults (57% females) aged older than 55 years from a cross-sectional study were included. A battery of PF test was performed, and participants were divided into 3 groups: low, medium and high fitness. Blood samples were collected, and subjects were also grouped based on a particular biomarker being within its reference range. Furthermore, drug intake and dietary intake were considered for each participant. Higher concentrations out of the reference range were observed for vitamin 25(OH)D (67.9%) and total cholesterol (TC) (58.6%). Participants from the low PF group presented lower significant concentrations out of the reference range for vitamin B12 and triglycerides; however, participants in the low PF group showed higher significant concentrations out of the reference range for total homocysteine, creatinine, TC, HDL-cholesterol and LDL-cholesterol (LDL-c) than those in the high PF group (all p<0.05). Considering drugs related to blood lipid modifications, subjects who regularly consumed lipid reducers presented higher significant concentrations out of the reference range for TC and LDL-c than participants who did not take these drugs (p<0.01). Participants from the high PF group presented better blood marker profiles, namely, lower blood markers related to disease risk out of the reference range. These blood markers could be used as a routine method for considering PF groups in older adults.