In a material-guided approach, instructive scaffolds that leverage potent chemistries may efficiently promote bone regeneration. A siloxane macromer has been previously shown to impart osteoinductivity and bioactivity when included in poly(ethylene glycol) diacrylate (PEG-DA) hydrogel scaffolds. Herein, phosphonated-siloxane macromers were evaluated for enhancing the osteogenic potential of siloxane-containing PEG-DA scaffolds. Two macromers were prepared with different phosphonate pendant group concentrations, poly(diethyl(2-(propylthio)ethyl)phosphonate methylsiloxane) diacrylate (PPMS-DA) and 25%-phosphonated analogue (PPMS-DA 25%). Macroporous, templated scaffolds were prepared by cross-linking these macromers with PEG-DA at varying mol % (15:85, 30:70, and 45:55 PPMS-DA to PEG-DA; 30:70 PPMS-DA 25% to PEG-DA). Other scaffolds were also prepared by combining PEG-DA with PDMS-MA (i.e., no phosphonate) or with vinyl phosphonate (i.e., no siloxane). Scaffold material properties were thoroughly assessed, including pore morphology, hydrophobicity, swelling, modulus, and bioactivity. Scaffolds were cultured with human bone marrow-derived mesenchymal stem cells (normal media) and calcium deposition and protein expression were assessed at 14 and 28 days.