This study reports the synthesis and characterization of x_MoO3/H-Z/S micro-mesoporous catalyst, which combines the properties of ZSM-5 and SBA-15, as well as its performance for biodiesel production from the transesterification of soybean oil. ZSM-5 was added to the SBA-15 synthesis gel, calcinated, and molybdenum trioxide (MoO3) was incorporated by incipient wetness using ammonium heptamolybdate salt [(NH4)6Mo7O24‧4H2O] as a metal precursor. The diffractograms and micrographics showed a micro-mesoporous structure of the support with the characteristic peaks of MoO3. The textural analysis showed that increasing the MoO3 content decreases the specific area and the pore diameter of the catalysts. The Raman spectrum of the catalysts indicated vibration modes characteristic of the active species MoO3 in the orthorhombic phase. The methanol/oil molar ratio was the variable that most influenced the yield of methyl esters within the levels of a design of experiments matrix. The highest biodiesel yield of 79.2% was obtained with 6 (wt.%) of MoO3, 4 h of reaction time, and a methanol/oil molar ratio of 20/1. This reaction condition uses a lower molybdenum content, lower catalyst load, and lower methanol/oil molar ratio than those reported in the literature, which qualitatively reduces the process costs. A quantitative economic analysis must be further performed to define the economic viability of the process.