Concerns about photodegradation products leaching from plastic bottle material into water during solar water disinfection (SODIS) are a major psychological barrier to increased uptake of SODIS. In this study, a comparison of SODIS efficacy using glass and plastic polyethylene terephalate (PET) bottles was carried out under strong real sunlight and overcast weather conditions at Makerere University in central Uganda. Both clear and turbid natural water samples from shallow wells and open dug wells, respectively, were used. Efficacy was determined from the inactivation of a wild strain of Escherichia coli in solar-exposed contaminated water in both glass and PET bottles. The studies reveal no significant difference in SODIS inactivation between glass and PET bottles (95% CI, p > 0.05), for all water samples under the different weather conditions except for clear water under overcast conditions where there was a small but significant difference (95% CI, p = 0.047) with less viable bacterial counts in PET bottles at two intermediate time points but not at the end of the exposure. The results demonstrate that SODIS efficacy in glass under tropical field conditions is comparable to PET plastic. SODIS users in these regions can choose either of reactors depending on availability and preference of the user.