Background: Dengue and chikungunya co-infections are an emerging threat to public health in tropical and subtropical areas. This study investigates acute and long-term clinical presentation patterns of chikungunya against a backdrop of preceding dengue infection and determines predicting factors for long-term chikungunya sequelae. Methods: A retrospective cohort study was performed in 2015, including 299 previously confirmed chikungunya cases, of which 162 subjects were assessed for dengue serology at disease onset. Results: Those with previous dengue infection (35.2% of the examined population) had a similar acute disease presentation, and suffered (not statistically significantly) more frequently from long-term musculoskeletal and neuropsychological symptoms compared to chikungunya-only patients. Patients with a preceding dengue infection (vs. those without) (OR = 4.17; p = 0.004), female sex (OR = 3.17; p = 0.034) and pre-existing joint disease (OR = 2.95; p = 0.031) had a higher risk of developing aggravated long-term chikungunya. Chronic disease (sequelae lasting > 90 days) was predicted by an age between 41 and 60 (OR = 3.07; p = 0.009) and concomitant cardiovascular disease (OR = 4.08; p = 0.010), but not by a preceding dengue infection. Conclusions: This study suggests several predicting factors of, and a possible link between preceding dengue and chikungunya infection and aggravated long-term sequelae, which should be interpreted in the light of the limitations of this study.