The development of three-dimensional (3D) fibrous networks as platforms for tissue engineering applications has been attracting considerable attention. Opportunely arranged microscaled fibers offer an appealing biomimetic 3D architecture, with an open porous structure and a high surface-to-volume ratio. The present work describes the development of modified-alginate hydrogel microfibers for cell entrapment, using a purpose-designed flow circuit. For microfibers biofabrication, cells were suspended in gel-precursor alginate solution and injected in a closed-loop circuit with circulating cross-linking solution. The flow promoted stretching and solidification of continuous cell-loaded micro-scaled fibers that were collected in a strainer, assembling into a microfibrous patch. The process was optimized to allow obtaining a self-standing cohesive structure. After characterization of the microfibrous patch, the behavior of embedded human mesenchymal stem cells (hMSCs) was evaluated. Microfibers of oxidized alginate modified with integrin-binding ligands provided a suitable 3D cellular microenvironment, supporting hMSCs survival and stimulating the production of endogenous extracellular matrix proteins, such as fibronectin and collagen Type I. Collectively, these features make the proposed microfibrous structures stand out as promising 3D scaffolds for regenerative medicine.