Background/Objectives: Chlorhexidine and iodine-based preparations are both widely used, and the existing literature suggests a possible advantage of chlorhexidine in clean elective surgery. Whether this extends to instrumented degenerative spine surgery is unknown. We asked whether chlorhexidine-based skin preparation reduces 90-day postoperative infection compared with iodine-based preparation after instrumented degenerative cervical or lumbar spine surgery. Methods: A retrospective TriNetX cohort study was performed among adults undergoing instrumented degenerative cervical or lumbar spine surgery. Patients were stratified by anatomic region and by preoperative preparation exposure: chlorhexidine-based versus iodine-based. Moreover, 1:1 propensity-score matching was performed within each anatomic stratum on demographics, Charlson Comorbidity Index (CCI), diabetes, smoking, obesity and BMI, immunosuppression, methicillin-resistant Staphylococcus aureus (MRSA) carrier status, and index procedure codes. The primary outcome was 90-day postoperative infection. Secondary outcomes were superficial and deep surgical site infection, MRSA infection, incision and drainage, debridement, sepsis, urinary tract infection, and pneumonia. Results: After matching, the cervical cohort included 3528 patients per group and the lumbar cohort 4164 per group. Postoperative infection did not differ in the cervical cohort (1.76% vs. 1.59%; risk ratio [RR] 1.11, 95% confidence interval [CI] 0.77–1.58; p = 0.578) or the lumbar cohort (3.17% vs. 3.29%; RR 0.96, 95% CI 0.76–1.22; p = 0.757). Superficial and deep infection, MRSA infection, debridement, sepsis, urinary tract infection, and pneumonia did not differ significantly in either cohort. Conclusions: No statistically significant difference in 90-day postoperative infection was found between chlorhexidine-based and iodine-based skin preparation after instrumented degenerative cervical or lumbar spine surgery.