In January 2016, health authorities from Zambézia province, Mozambique reported the detection of some patients presenting with fever, arthralgia, and a positive result for chikungunya in an IgM-based Rapid Diagnostic Test (RDT). We initiated a study to investigate a potential chikungunya outbreak in the city of Quelimane. Methods/Principal findings From February to June 2016, we conducted a cross-sectional study enrolling febrile patients attending five outpatient health units in Quelimane. Serum from each patient was tested for CHIKV and DENV, using IgM and IgG ELISA and qRT-PCR. Patients were also tested for malaria by RDT. Entomological surveys were performed around patients' households, and we calculated the proportion of positive ovitraps and the egg density per trap. A total of 163 patients were recruited, of which 99 (60.7%) were female. The median age was 28 years. IgM and IgG anti-CHIKV antibodies were identified in 17 (10.4%) and 103 (63.2%) patients, respectively. Plaque reduction neutralization assay confirmed the presence of anti-CHIKV antibodies in a subset of 11 tested patients with positive IgG results. IgM anti-DENV antibodies were found in 1 (0.9%) of 104 tested patients. Malaria was diagnosed in 35 (21.5%) patients, 2 of whom were also IgM-positive for CHIKV. Older age and lower education level were independently associated with the prevalence of IgG anti-CHIKV antibodies. Immature forms of Aedes aegypti were collected in 16 (20.3%) of 79 surveyed households. We also found that 25.0% (16/64) of the traps were positive, with an average of 90.8 eggs per pallet. Conclusions Our investigation demonstrated that no CHIKV outbreak was ongoing in Quelimane; rather, endemic transmission of the virus has been ongoing. Aedes aegypti mosquitoes are abundant, but dengue cases occurred only sporadically. Further population-based cohort studies are needed to improve our understanding of aspects related to the dynamics of arboviral transmission in Mozambique, as well as in other parts of Sub-Saharan Africa.