The aesthetics and functionality of honeycomb woven assemblies qualifies them for a range of applications expanding across home textiles, fashion, functional apparels, and technical products. Researchers have explored honeycomb assemblies with the focus on shrinkage, sound absorption, thermal conductivity, and heat protection properties analysis via variation in their cell sizes. However, very minimal research is found on analysis of honeycomb woven fabric assemblies’ thermal comfort characteristics by employing different weft insertion sequence and materials (cotton and stretchable yarns). This study reflects the thermal conductivity, dry fluid transmission (air permeability), wet fluid transmission (moisture management), and stiffness attributes of twelve stretchable honeycomb woven assemblies consisting of single ridge, double ridge, and brighton honeycomb weave structures along with different weft sequences of cotton and Type 400 (T-400) stretch yarns. Characterization data showed that single ridge honeycomb structure supports the highest dry fluid transmission property; however, brighton honeycomb offers the highest heat retention property. Double ridge honeycomb highlights the capability of the highest wet fluid transmission property, and brighton honeycomb has immense stiffness. Statistical analysis (ANOVA) also showed that honeycomb structures, weft yarn sequence and material have a statistically significant impact on thermal conductivity and fluid transmission behaviors with p-values less than 0.05.