In Ecuador, a national program for bovine brucellosis control has been in implementation since 2008. Given the costs, small- and medium-sized livestock holders are not completely committed to it. The objective of this study was to determine true prevalence (TP) of bovine brucellosis in small- and medium-sized herd populations, as well as the diagnostic sensitivity and specificity of the Rose Bengal (RB) test and the sero-agglutination test (SAT)-EDTA using a Bayesian approach. Between 2011 and 2016, 2733 cattle herds were visited, and 22,592 animal blood samples were taken in nineteen provinces on mainland Ecuador. Bayes-p and deviance information criterion (DIC) statistics were used to select models. Additionally, risk-factor analysis was used for herds according to their brucellosis test status. True prevalence (TP) in herds was estimated by pool testing. National seroprevalence of farms was 7.9% (95% CI: 6.79-9.03), and TP was 12.2% (95% CI: 7.8-17.9). Apparent prevalence (AP) in animals was 2.2% (95% CI: 1.82-2.67), and TP was 1.6% (95% CrI: 1.0-2.4). Similarly, the sensitivity of the RB was estimated at 64.6% (95% CrI: 42.6-85.3) and specificity at 98.9% (95% CrI: 98.6-99.0); for the SAT-EDTA test, sensitivity was 62.3% (95% CrI: 40.0-84.8) and 98.9% (95% CrI: 98.6-99.1) for specificity. Results of the two tests were highly correlated in infected and uninfected animals. Likewise, high spatial variation was observed, with the Coastal Region being the zone with the highest TP at 2.5%. (95% CrI: 1.3-3.8%) in individual animals and 28.2% (95% CI: 15.7-39.8) in herds. Risk factors include herd size, type of production (milk, beef, and mixed), abortions recorded, and vaccination. The results of this study serve to guide authorities to make decisions based on parallel testing at the beginning of a bovine brucellosis program for small livestock holders to increase sensitivity level of the screening tests in Ecuador.