Gradual replacement of the traditional raw materials in polyurethane (PU) synthesis by bio-based ones and introduction of environmentally friendly physical blowing agents (PBAs) motivate the analysis of thermal aging of bio-based foams in order to optimize the chemical structure of the PU matrix so that its permeability to PBA is minimized. With the aim of elucidating the effect of the PU chemical structure on thermal aging of foams, rigid low-density closed-cell PU foams were produced solely from bio-based polyols. The effective diffusivities of PBA and atmospheric gasses were evaluated based on the measured thermal conductivity aging of foams and validated by gas chromatography measurements of gas composition in foam cells. Gas permeability of the PU polymer was estimated based on effective diffusivity in foams and foam morphology and found to decrease with increasing crosslink density, apparently due to reduction in the fractional free volume in the polymers.