Biomaterial properties and controlled architecture of scaffolds are essential features to provide an adequate biological and mechanical support for tissue regeneration, mimicking the ingrowth tissues. In this study, a bioextrusion system was used to produce 3D biodegradable scaffolds with controlled architecture, comprising three types of constructs: (i) poly(ε-caprolactone) (PCL) matrix as reference; (ii) PCL-based matrix reinforced with cellulose nanofibers (CNF); and (iii) PCL-based matrix reinforced with CNF and hydroxyapatite nanoparticles (HANP). The effect of the addition and/or combination of CNF and HANP into the polymeric matrix of PCL was investigated, with the effects of the biomaterial composition on the constructs (morphological, thermal, and mechanical performances) being analysed. Scaffolds were produced using a single lay-down pattern of 0/90°, with the same processing parameters among all constructs being assured. The performed morphological analyses showed a satisfactory distribution of CNF within the polymer matrix and high reliability was obtained among the produced scaffolds. Significant effects on surface wettability and thermal properties were observed, among scaffolds. Regarding the mechanical properties, higher scaffold stiffness in the reinforced scaffolds was obtained. Results from the cytotoxicity assay suggest that all the composite scaffolds presented good biocompatibility. The results of this first study on cellulose and hydroxyapatite reinforced constructs with controlled architecture clearly demonstrate the potential of these 3D composite constructs for cell cultivation with enhanced mechanical properties.