Background: Chikungunya, and Zika emerged in the 2010s in the Americas, causing simultaneous epidemics with dengue. However, little is known of theseAedes-borne diseases (ABDs) joint patterns and contributors at the population-level. Methods: We applied a novel Poisson-multinomial spatial model to the registered cases of dengue (n=291,820), chikungunya (n=75,913), and Zika (n=72,031) by municipality in Colombia, 2014-2016. This model estimates the relative risk of total ABDs cases and associated factors, and, simultaneously, the odds of presence and contributors of each disease using dengue as a baseline category. This approach allows us to identify combined characteristics of ABDs, since they are transmitted by the same mosquitoes, while also identifying differences between them. Findings: We found an increased ABDs risk in valleys and south of the Andes, the Caribbean coast, and borders, with temperature as the main contributor (Relative Risk 2.32, 95% Credible Interval, CrI, 2.05-2.64). Generally, dengue presence was the most probable among the ABDs, although that of Zika was greater on Caribbean islands. Chikungunya and Zika were more likely present than dengue in municipalities with less vegetation (Odds Ratio, OR, 0.75, 95%CrI 0.65-0.86, and 0.85, 95%CrI 0.74-0.99, respectively). Chikungunya tended to be present in more socially vulnerable areas than dengue (OR 1.20, 95%CrI 0.99-1.44) and Zika (OR 1.19, 95%CrI 0.95-1.48). Interpretation: Important differences between the ABDs were identified and can help guide local and context-specific interventions, such as those aimed at preventing cases importation in border and tourism locations and reducing chikungunya burden in socially vulnerable regions.