Scaffolds based on chitosan/polygalacturonic acid (ChiPgA) complex containing montmorillonite (MMT) clay modified with 5-aminovaleric acid were prepared using freeze-drying technique. The MMT clay was introduced to improve mechanical properties of the scaffold. The microstructure of the scaffolds containing the modified MMT clay was influenced by the incorporation of nanoclays. The MTT assay also indicated that the number of osteoblast cells in ChiPgA scaffolds containing the modified clay was comparable to ChiPgA scaffolds containing hydroxyapatite known for its osteoconductive properties. Overall, the ChiPgA composite scaffolds were found to be biocompatible. This was also indicated by the scanning electron microscopy images of the ChiPgA composite scaffolds seeded with human osteoblast cells. Photoacoustic–Fourier transform infrared (PA-FTIR) experiments on the ChiPgA composite scaffolds indicated formation of a polyelectrolyte complex between chitosan and polygalacturonic acid. PA-FTIR studies also showed that the MMT clay modified with 5-aminovaleric acid was successfully incorporated in the ChiPgA based scaffolds. Swelling studies on ChiPgA composite scaffolds showed the swelling ability of the scaffolds that indicated that the cells and the nutrients would be able to reach the interior parts of the scaffolds. In addition to this, the ChiPgA scaffolds exhibited porosity greater than 90% as appropriate for scaffolds used in tissue engineering studies. High porosity facilitates the nutrient transport throughout the scaffold and also plays a role in the development of adequate vasculature throughout the scaffold. Compressive mechanical tests on the scaffolds showed that the ChiPgA composite scaffolds had compressive elastic moduli in the range of 4–6 MPa and appear to be affected by the high porosity of the scaffolds. Thus, the ChiPgA composite scaffolds containing MMT clay modified with 5-aminovaleric acid are biocompatible. Also, the ChiPgA scaffolds containing the modified MMT clay appears to satisfy some of the basic requirements of scaffolds for tissue engineering applications.