In the context of filovirus outbreaks, chlorine spraying has been the standard for infection prevention and control. Due to potential occupational health risks, public health institutions now recommend wiping, which is labor-intensive and may increase the risk of heat stress for healthcare workers wearing personal protective equipment. This systematic review and meta-analysis quantified the health effects of occupational exposure to chlorine-based products compared to other disinfectants, and the effects of spraying compared to general disinfection tasks (GDTs) like wiping and mopping, in healthcare settings. MEDLINE, Scopus, and ScienceDirect were searched for studies addressing the association between exposure to disinfectants applied by different application methods and occupational diseases in healthcare settings. Risk of bias was assessed by two independent reviewers using a validated tool. Two reviewers independently screened and performed data extraction and synthesis. A third reviewer resolved disagreements. Meta-analyses were conducted using fixed- and random-effects models based on the Higgins I2 statistic. 30 studies investigating chlorine-based products (7,123 participants), glutaraldehyde (6,256 participants), peracetic acid, acetic acid and hydrogen peroxide (4,728 participants), quaternary ammonium compounds (QACs) (9,270 participants), use of spray (4,568 participants) and GDTs (3,480 participants) were included. Most had a cross-sectional design and high risk of bias. Meta-analysis indicates a significant association between respiratory conditions and exposure to chlorine-based products (OR 1.71, 95%CI 1.41-2.08), glutaraldehyde (OR 1.44, 95%CI 1.14-1.81), QACs (OR 1.30, 95%CI 1.06-1.60), use of spray (OR 2.25, 95%CI 1.61-3.14) and GDTs (OR 2.20, 95%CI 1.66-2.90). The relative odds ratio (ROR) of respiratory conditions for chlorine-based products compared to QACs was 0.76 (95%CI 0.62-0.94). The ROR for the use of spray compared to GDTs was 0.98 (95%CI 0.74-1.29). Strengths include evaluating respiratory health risks of disinfectants, applying a validated tool, using both fixed- and random-effects models, and comparing pooled effect sizes. Limitations include high risk of bias for the majority of included articles, varying confounder adjustments, underreported non-respiratory outcomes, and unspecified disinfectants and PPE use for spray and GDTs articles. Chlorine-based disinfectants significantly increase respiratory risk compared to QACs. Sprays and general disinfection tasks present similar risks. Our findings advocate for using less hazardous products like QACs, rather than banning sprays in filovirus outbreak responses to enhance disinfection safety. CRD42023479363.