Novel water tolerant sulfonic acid based Periodic Mesoporous Organosilicas (PMOs) having either phenylene (1a) or ethyl (1b) as bridge and methylpropyl sulfonic acid as functionalized group have been developed. The materials have been then employed in efficient biodiesel production via direct transesterification of sunflower oil, canola oil, corn oil, refined olive oil, and extracted oil from olive sludge with methanol. By comparing the catalytic performance of these acids with well-known SBA-15-PrSO3H, it was revealed that catalyst 1b bearing an ethyl bridging group is a more reactive catalytic system in biodiesel production. On the other hand, while the water adsorption experiment shows that among the described PMO functionalized acids, 1a shows more hydrophobic character, in contrast, we interestingly found that 1b consistently exhibited higher catalytic performance in biodiesel formation, which relies on a balance between hydrophobic-hydrophilic- and pore size of the mesochannels in this catalyst.