Microfluidic devices serve as essential tools across diverse fields like medicine, biotechnology, and chemistry, enabling advancements in analytical techniques, point-of-care diagnostics, microfluidic cell cultures, and organ-on-chip models. While polymeric microfluidics are favoured for their cost-effectiveness and ease of fabrication, their inherent hydrophobic properties necessitate surface functionalization, often post-sealing. Here, we introduce a versatile apparatus for functionalizing sealed microfluidic devices using atmospheric plasma processing, with a focus on PDMS (polydimethylsiloxane) microfluidics. Through meticulous analysis of surface properties and capillary speed, before and after plasma treatment, along with a comparison between vacuum and atmospheric plasma functionalization methods, we demonstrate the efficacy of our approach. Subsequent experimentation within 3D PDMS microfluidic chambers, combining atmospheric pressure plasma treatment with collagen coating to facilitate mesenchymal stem cells (MSCs) growth over five days, reveals enhanced initial cell adhesion and proliferation, highlighting the potential of our method for improving cell-based applications within microfluidic systems.