Composites made of plant residues from agricultural and forestry productions offer unique environmental, health, and socioeconomic benefits as construction materials. However, controlling the porosity and surface conditions of building enclosures crucial to preventing moisture and deterioration pervasiveness during and post-flooding remains a challenge. Fused deposition modelling can enable lightweight components to be produced with customised designs and functionalities for use in construction panels including in flood risk zones. Unlike other 3D printing processes, FDM involves only melting and extrusion, rendering it advantageous for plant residue composites. But are FDM products scalable and factually resilient for construction applications as in sites subject to flooding? We lack knowledge on sorptivity properties or size increase implications on material functionalities. Advancing our understanding of mechanic-structure interdependence and size increase effects is critical to overcoming scalability hurdles essential for exterior construction applications. Experimental research methods were implemented from the nano-micro to the integral scale to identify porosity, particle-binder interface, thermal, and sorptivity properties. Bio-based thermoplastics PLA-PHA blends recognized in literature and industry as the most efficient FDM matrices were chosen. Residues of bamboo and cork were selected as fillers of PLA-PHA matrices due to their combined waste production volume output, microstructure diversity, and unique mechanical, thermal, water uptake properties and their use in commercial FDM filaments. The transitional border of the Northwestern Amazon was used as a riparian context under severe socioeconomic and flood risk impact with a long tradition of plant-based building enclosures. This study constitutes the first evaluation of FDM composites under wet-dry cycles across all length scales. Cork composites displayed superior water and thermal resistance than bamboo composites showing potential as exterior panels in flood contexts. The research identified that the strength stiffness properties of cork-PLA-PHA versus bamboo-PLA-PHA composites are reversed compared to natural cork and bamboo, showing these were not affected equally by processing and size increase. This investigation demonstrated the significance of experimentally assessing from the plant cell interface to the integral scale products informed by quantitative and qualitative contextual factors. Integrative experimental protocols are crucial to determine FDM’s potential for carbon neutral construction composites.