The floods associated with the landfall of cyclones Idai and Kenneth in Mozambique between March and April 2019 had a major impact on the country’s public health and placed the affected population at risk for vector- and rodent-borne diseases. Aiming to improve the diagnostic capacity, yield information to guide public health responses, and assess potential short-term effects of cyclones Idai and Kenneth on arboviruses (dengue, Zika, and chikungunya) and leptospirosis, we established a clinical and laboratory surveillance for non-malarial acute febrile illness in six health units located in different districts within the two provinces (Sofala and Cabo Delgado) most affected by the cyclones. Patients were tested by real-time reverse transcriptase polymerase chain reaction (qRT-PCR) for dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) viruses and by enzyme immunoassay (ELISA) to detect nonstructural DENV protein 1 (NS1) and DENV, ZIKV, CHIKV, and Leptospira IgM antibodies. From April to September 2019, we enrolled 305 patients aged ≥15 years, of which 58.4% were women and the median age was 30 years. All patients were qRT‐PCR negative for arboviruses. Three (1.0%) patients were positive by DENV NS1 ELISA. Specific IgM antibodies against DENV, ZIKV, CHIKV, or Leptospira were found in the serum of 104 (34.1%) patients. Our results indicate that vector- and rodent-borne diseases transmission occurred in all districts under investigation on the wake of cyclones Idai and Kenneth, including some regions of the country where cases had not been previously detected. The investigation provided useful information for post-cyclone emergency response purposes.