Egg consumers worldwide have increased their concerns about laying hens’ welfare and its impact on final egg product quality. This study compared the egg quality parameters under the conventional cage (CC) and cage-free (CF) egg production systems in the tropics. The study was conducted on a commercial farm in Colombia using Hy-Line Brown pullets, reared under the same conditions for the first 15 wks. At 16 wks, the hens were distributed into two housing systems, CC and CF, on the same farm. The hens were fed the same diet for each phase in both systems and feed intake varied slightly. Egg samples were collected every six wks, from 22 to 82 wks of age. A total of 3960 eggs were analyzed at 11 sampling times. Parameters such as albumen height, egg weight, yolk color, eggshell thickness, eggshell strength, and Haugh units were determined using a DET-6000 machine. At 22 and 82 wks, screening for Salmonella spp. status was conducted using environmental and egg samples. Additionally, at 34, 64, and 82 wks, yolk samples were obtained for fatty acid profiles and crude protein (CP) analysis. The data were analyzed in a completely randomized block design with repeated measures (11 times): mean separation by Student’s t-test yolk pigmentation, Haugh Units, and albumen height (p < 0.001) were higher in the CF compared with the CC between 38 and 69 wks of age, and eggs at 63 and 82 wks (p < 0.05) were heavier in the CF compared to the CC. Likewise, eggs from the CC had better eggshell strength from 57 to 82 wks. In the egg yolk fatty acid profile at the 34th wk, the pentadecanoic, palmitic, and heptadecanoic acids had higher concentrations in the CF systems than the CC. At the 64th wk, the egg yolk fatty acids—lauric, myristic, and heptadecanoic—had higher concentrations in the CF; likewise, at the 82nd wk, egg yolks from the CC had higher concentrations of lauric, heptadecanoic, and nervonic fatty acids than the CF. The eggs and environmental samples were negative for Salmonella spp. throughout the whole production phase. These results indicated that the production system might impact internal and external egg quality measures, potentially due to various stressors, including environmental factors or behavior restrictions.