The objective of this work was to investigate material properties and osteogenic differentiation of human mesenchymal stem cells (hMSCs) in genipin (GN) crosslinked chitosan/nano β-tricalcium phosphate (CS/nano β-TCP) scaffolds, and compare the results with tripolyphosphate (TPP) crosslinked scaffolds. Porous crosslinked CS/nano β-TCP scaffolds were produced by freeze-gelation using GN (CBG scaffold) and TPP (CBT scaffold) as crosslinkers. The prepared CBT and CBG scaffolds were characterized with respect to porosity, pore size, water content, wettability, compressive strength, mass loss, and osteogenic differentiation of hMSCs. All scaffolds displayed interconnected honeycomb-like microstructures. There was a significant difference between the average pore size, porosity, contact angle, and percent swelling of CBT and CBG scaffolds. The average pore size of CBG scaffolds was higher than CBT, the porosity of CBG was lower than CBT, the water contact angle of CBG was higher than CBT, and the percent swelling of CBG was lower than CBT. At a given crosslinker concentration, there was not a significant difference in compressive modulus and mass loss of CBG and CBT scaffolds. Metabolic activity of hMSCs seeded in CBG scaffolds was slightly higher than CBT. Furthermore, CBG scaffolds displayed slightly higher extent of mineralization after 21 days incubation in osteogenic medium compared to CBT.