The production of medical devices follows strict guidelines where bio- and hemocompatibility, mechanical strength, and tear resistance are important features. Segmented polyurethanes (PUs) are an important class of polymers that fulfill many of these requirements, thus justifying the investigation of novel derivatives with enhanced properties, such as modulated carbon dioxide and oxygen permeability. In this work, three segmented polyurethane-based membranes, containing blocks of hard segments (HSs) dispersed in a matrix of soft segment (SS) blocks, were prepared by reacting a PU prepolymer (PUR) with tris(hydroxymethyl)aminomethane (TRIS), Congo red (CR) and methyl-β-cyclodextrin (MBCD), rendering PU/TRIS, PU/CR and PU/MBCD membranes. The pure (control) PU membrane exhibited the highest degree of phase segregation between HSs and SSs followed by PU/TRIS and PU/MBCD membranes, and the PU/CR membrane displayed the highest degree of mixing. Pure PU and PU/CR membranes exhibited the highest and lowest values of Young’s modulus, tangent moduli and ultimate tensile strength, respectively, suggesting that the introduction of CR increases molecular mobility, thus reducing stiffness. The CO₂ permeability was highest for the PU/CR membrane, 347 Barrer, and lowest for the pure PU membrane, 278 Barrer, suggesting that a higher degree of mixing between HSs and SSs leads to higher CO₂ permeation rates. The permeability of O₂ was similar for all membranes, but ca. 10-fold lower than the CO₂ permeability.