In this study, we developed iron oxide based magnetic nanoparticles (MNPs) by precipitation of iron salts in the presence of ammonia and created four different formulations: without functionality (plain MNPs, no coating), with beta-cyclodextrin (MNPs+beta-CD) or pluronic 127 polymer (MNPs+F-127), and both beta-cyclodextrin and pluronic 127 polymer (MNPs+beta-CD-F-127) functionality for its efficient use in mucosal delivery. We studied the interaction and/or binding behavior of these MNPs formulations with porcine stomach mucin using steady-state fluorescence spectroscopy, and then quantified the bound mucin from absorption studies. Toxicity of these MNPs against cervical cancer cells and red blood cells was evaluated. Ex-vivo studies were performed using freshly collected gastrointestinal, ovarian, pancreas and colon organ tissues of pig to evaluate binding and uptake phenomenon of MNPs. Transport studies of these MNPs in mucin was evaluated using Boyden's chamber assay. All these studies together suggest that the MNPs+beta-CD-F-127 formulation was strongly interacted with mucin and interestingly transported through mucin compared to other MNPs formulations. Hence, MNPs+beta-CD-F-127 formulation could be a good candidate for the mucoadhesive biopharmaceuticals and drug delivery system. (C) 2016 Published by Elsevier Inc.