Quality improvements and reduction of disease risk for low-resource shared sanitation facilities require cleanliness assessment approaches that are both rigorous and practical. Using Adenosine Triphosphate (ATP) bioluminescence testing, we assessed contamination on high-touch (HT) surfaces (inner door handles) at 32 shared toilet sites in Kisumu, Kenya. In public toilets, contamination was lowest after cleaning and disinfection (C&D) with 0.5% chlorine solution (adjusted difference in mean log10 Relative Light Units per 100 cm2 (aDiff): −1.61; CI: −2.43, −0.59), followed by C&D with 0.1% chlorine solution (aDiff: −1.16; CI: −1.77, −0.55). ATP levels were not associated with overall observable toilet cleanliness and had poor agreement with visually assessed HT surface cleanliness. Our findings demonstrate the utility of this field-feasible method for detecting the impact of recent C&D in low-resource shared toilets, a novel setting for ATP cleanliness testing, while also highlighting the importance of using effective C&D procedures and addressing HT surfaces within cleaning protocols.