Protein separation is an integral step in biopharmaceutical manufacture with diffusion-limited packed bed chromatography remaining the default choice for industry. Rapid bind-elute separation using convective mass transfer media offers advantages in productivity by operating at high flowrates. Electrospun nanofibre adsorbents are a non-woven fibre matrix of high surface area and porosity previously investigated as a bioseparation medium. The effects of compression and bed layers, and subsequent heat treatment after electrospinning cellulose acetate nanofibres were investigated using diethylaminoethyl (DEAE) or carboxylate (COO) functionalisations. Transbed pressures were measured and compared by compression load, COO adsorbents were 30%, 70% and 90% higher than DEAE for compressions 1, 5 and 10 MPa, respectively, which was attributed to the swelling effect of hydrophilic COO groups. Dynamic binding capacities (DBCs) at 10% breakthrough were measured between 2000 and 12 000 CV/h (2 s and 0.3 s residence times) under normal binding conditions, and DBCs increased with reactant concentration from 4 to 12 mg BSA/mL for DEAE and from 10 to 21 mg lysozyme/mL for COO adsorbents. Comparing capacities of compression loads applied after electrospinning showed that the lowest load tested, 1 MPa, yielded the highest DBCs for DEAE and COO adsorbents at 20 mg BSA/mL and 27 mg lysozyme/mL, respectively. At 1 MPa, DBCs were the highest for the lowest flowrate tested but stabilised for flowrates above 2000 CV/h. For compression loads of 5 MPa and 10 MPa, adsorbents recorded lower DBCs than 1 MPa as a result of nanofibre packing and reduced surface area. Increasing the number of bed layers from 4 to 12 showed decreasing DBCs for both adsorbents. Tensile strengths were recorded to indicate the mechanical robustness of the adsorbent and be related to packing the nanofibre adsorbents in large scale configurations such as pleated cartridges. Compared with an uncompressed adsorbent, compressions of 1, 5 and 10 MPa showed increases of 30%, 110% and 110%, respectively, for both functionalisations. The data presented show that capacity and mechanical strength can be balanced through compression after electrospinning and subsequent is particular to different functionalisations. This trade-off is critical to the development of nanofibre adsorbents into different packing configurations for application and scale up in bioseparation.