The n-3 index has been proposed as a risk factor for CVD endpoints. However, the association of the O3I defined with different cut-offs and cardiometabolic risk factors has been less studied. This study aimed to investigate the association between two cut-off points of the O3I and cardiometabolic risk factors in Brazilian and Puerto Rican adults. This cross-sectional analysis included 249 Brazilians and 1261 Puerto Ricans, aged 45–75 years. Fatty acids composition was quantified in erythrocyte membranes using GC with a flame ionisation detector. The O3I was categorised as ≤ 4 % (low), > 4–8 % (intermediate) and ≥ 8 % (desirable), and as ≤ 4 % (very low), > 4–6 % (low), > 6–8 % (moderate) and > 8 % (high) in the second cut-off classification. Serum lipids, waist circumference and insulin resistance were measured from standardised protocols. Multivariable-adjusted linear models tested the association between the O3I and cardiometabolic factors. Brazilians had a mean (sd) O3I of 4·65 % (1·19 %) v. 4·43 % (1·14 %) in Puerto Ricans (P = 0·033), with only 1·6 % of Brazilians and 1·2 % of Puerto Ricans presenting a desirable/high O3I. The O3I, as continuous or for > 4 % (v. ≤ 4 %), was inversely associated with TAG, VLDL and TAG/HDL-cholesterol ratio in Puerto Ricans. In Brazilians, an O3I > 6 % (v. ≤ 6 %) was associated with higher total cholesterol, LDL-cholesterol and non-HDL-cholesterol. Both populations presented O3I below the desirable levels, and the magnitude and direction of associations with cardiometabolic factors varied by study and cut-offs, reinforcing the importance of expanding these investigations to more diverse populations.