Professional skilled care has shown to be one of the most promising strategies to reduce maternal mortality, and in-facility deliveries are a cost-effective way to ensure safe births. Countries in Mesoamerica have emphasized in-facility delivery care by professionally skilled attendants, but access to good-quality delivery care is still lacking for many women. We examined the characteristics of women who had a delivery in a health facility and determinants of the decision to bypass a closer facility and travel to a distant one. We used baseline information from the Salud Mesoamerica Initiative (SMI). Data were collected from a large household and facilities sample in the poorest quintile of the population in Guatemala, Honduras and Nicaragua. The analysis included 1592 deliveries. After controlling for characteristics of women and health facilities, being primiparous (RR ¼ 1.15, 95% CI 1.10, 1.21), being literate (RR ¼ 1.24, 95% CI 1.04, 1.48), having antenatal care (RR ¼ 1.68, 95% CI 1.24, 2.27), being informed of the need for having a C-section (RR ¼ 1.07, 95% CI 1.02, 1.11) and travel time to the closest facility totaling 1-2 h vs under 30 min (RR ¼ 0.88, 95% CI 0.77, 0.99) were associated with in-health facility deliveries. In Guatemala, increased availability of medications and equipment at a distant facility was strongly associated with bypassing the closest facility in favor of a distant one for delivery (RR ¼ 2.10, 95% CI 1.08, 4.07). Our study showed a strong correlation between well-equipped facilities and delivery attendance in poor areas of Mesoamerica. Indeed, women were more likely to travel to more distant facilities if the facilities were of higher level, which scored higher on our capacity score. Our findings call for improving the capacity of health facilities, quality of care and addressing cultural and accessibility barriers to increase institutional delivery among the poor population in Mesoamerica.