Recently, pollen grains (PGs) have been introduced as drug carriers and scaffolding building blocks. This study aimed to assess the in-vitro biocompatibility of Pistacia vera L. hollow PGs/Fe3O4 nanoparticles (HPGs/Fe3O4NPs) composites using human adipose-derived mesenchymal stem cells (hAD-MSCs). In this regard, iron oxide nanoparticles (Fe3O4NPs) were assembled on the surface of HPGs at different concentrations. The biocompatibility of the prepared composites was assessed through MTT assay, apoptosis-related gene expression and field emission scanning electron microscopy (FE-SEM) analysis. Compared to the bare HPGs, the HPGs/Fe3O4NPs exhibited a biphasic impact on hAD-MSCs. The composite containing 1% Fe3O4NPs demonstrated no cytotoxicity up to 21 days while higher Fe3O4NPs contents and long-term exposure revealed adverse effects on the hAD-MSCs’ growth. The obtained result was verified by the qRT-PCR and morphological analysis carried out through FE-SEM which suggests that a narrow region below 1% Fe3O4NPs may be the optimum choice for medicinal applications of HPGs/Fe3O4NPs microdevices.