The lack of ideal non-viral gene carriers has motivated the combination of delivery systems and tissue-engineered scaffolds, which may offer relevant advantages such as enhanced stability and reduced toxicity. In this work, we evaluated a new combination between niosome non-viral vectors and hyaluronic acid (HA) hydrogel scaffolds, both widely studied due to their biocompatibility as well as their ability to incorporate a wide variety of molecules. We evaluated three different niosome formulations (niosomes 1, 2 and 3) varying in composition of cationic lipid, helper lipid and non-ionic tensioactives. Niosomes and nioplexes obtained upon the addition of plasmid DNA were characterized in terms of size, polydispersity, zeta potential and ability to transfect mouse bone marrow cloned mesenchymal stem cells (mMSCs) in 2D culture. Niosome 1 was selected for encapsulation in HA hydrogels due to its higher transfection efficiency and the formulation was concentrated in order to be able to incorporate higher amounts of DNA within HA hydrogels. Nioplex-loaded HA hydrogels were characterized in terms of biomechanical properties, particle distribution, nioplex release kinetics and ability to transfect encapsulated mMSCs in 3D culture. Our results showed that nioplex-loaded HA hydrogel scaffolds presented little or no particle aggregation, allowed for extensive cell spreading and were able to efficiently transfect encapsulated mMSCs with high cellular viability. We believe that the knowledge gained through this in vitro model can be utilized to design novel and effective platforms for in vivo local and non-viral gene delivery applications.