Collagen biomaterials are widely used for soft tissue augmentation. Cross‐linking techniques for collagen matrix (CM) achieve mechanical and volumetric stability; nevertheless, cross‐linking may compromise biocompatibility. The aim of the present study was to investigate two different three‐dimensional (3D) porcine‐derived CMs, noncross‐linked (ncl)_CM and cross‐linked (cl)_CM, for their effects on macrophages (Mφ) and gingival fibroblasts. The effects of the CMs on the cell viability, proliferation, and polarization of Mφ derived from human monocyte THP‐1 cells were assessed. The effects of paracrine factors from Mφ cultured on the CMs were further studied in human gingival fibroblasts (HGF‐1 cells). The spongy layer of ncl_CM was partially resorbed after 1 day of culture. cl_CM maintained increased numbers of viable cells when compared with ncl_CM on day 3 for both THP‐1 and HGF‐1 cells. Higher mRNA levels of M1 markers, including IL‐1 and IL‐6, were found in Mφ cultured on cl_CM, while no significant differences were observed in M2 marker expression levels, including Arg1 and CD206, for cells cultured on both CMs when compared with those of the control. Furthermore, the conditioned medium collected from Mφ cultured on both CMs decreased cell viability. Nevertheless, neither of the CM‐conditioned media influenced the mRNA levels of TGF‐β, COL1a2, and PDGF‐A in HGF‐1 cells when compared with the control media. A comparison showed that cl_CM tended to result in more viable cells than ncl_CM, while cl_CM polarized Mφ toward an M1 phenotype, which was confirmed by the observation of increased mRNA levels of pro‐inflammatory cytokines.