Background The aim of this study was to investigate the effects of spinal stabilization exercises, chiropractic spinal manipulation and their combination on endurance, muscle strength, joint position sense, and balance in healthy individuals. Methods Eighty healthy people aged 18–45 years were included in the study. Participants in the study were randomly divided into 4 groups. Group 1 underwent 6 sessions of chiropractic manipulation. Instrument-assisted chiropractik manipulation was used. Group 2 underwent 18 sessions of stabilization exercises. Group 3 received both stabilization exercises and chiropractic manipulation. Group 4 was followed as the control group. Participants were evaluated with prone plank, side plank, Sorenson test, quadriceps muscle strength, knee joint position sense, and Y balance test before, after and 1 month after the application. Results After the application, significant improvements were observed in the prone and side plank parameters in Group 3 compared to Group 1 and Group 4, while a significant improvement was observed in the Sorenson parameter compared to Group 1 and Group 2. In addition, significant increases were found in quadriceps muscle strength in Group 1, Group 2 and Group 3 compared to Group 4. Conclusion Spinal stabilization exercise program applied together with chiropractic manipulation in healthy individuals may be more effective in improving muscular endurance and balance compared to other training programs. All training programs are effective in improving quadriceps muscle strength, but do not have the same effect on knee joint position sense. Trial registration: The study was also registered on ClinicalTrial.gov (Registration number: NCT04830098).