Introduction The surge of the COVID-19 pandemic challenged health services globally, and in Lesotho, the HIV and tuberculosis (TB) services were similarly affected. Integrated, multi-disease diagnostic services were proposed solutions to mitigate these disruptions. We describe and evaluate the effect of an integrated, hospital-based COVID-19, TB and HIV screening and diagnostic model in two rural districts in Lesotho, during the period between December 2020 and August 2022. Methods Adults and children above 5 years attending two hospitals were screened for COVID-19 and TB symptoms. After a positive screening, participants were offered to enroll in a service model that included clinical evaluation, chest radiography, SARS-CoV-2, Xpert MTB/RIF Ultra and HIV testing. Participants diagnosed with COVID-19, TB, or HIV were contacted after 28 days evaluate their health status, and linkage to HIV or TB services. Results Of the 179160 participants screened, 6623(37%) screened positive, and 4371(66%) were enrolled in this service model, yielding a total of 458 diagnoses. One positive rapid antigen test for SARS-CoV-2 was found per 11 participants screened, one Xpert-positive TB case was diagnosed per 85 people screened, and 1 new HIV diagnosis was done per 182 people screened. Of the 321(82.9%) participants contacted after 28 days of diagnosis, 304(94.7%) reported to be healthy. Of the individuals that were newly diagnosed with HIV or TB, 18/24(75.0%) and 46/51(90.1%) started treatment. This service showed no difference in the detection of new HIV and TB cases when compared to other hospitals, where no such integrated service model was provided. Conclusion This screening and diagnostic model successfully maintained same-day, integrated COVID-19, TB, and HIV testing services through different COVID-19 incidence periods in a resource-limited context. There were positive effects in avoiding diagnostic delays and ensuring linkage to services, however, efficiencies were contingent on the successful adaptation to the changing environment.