Cross-flow microfiltration of fast pyrolysis bio-oil is a physical treatment pathway capable of reducing the filtered product's solids content to acceptable levels for fuel utilization and/or upgrading. However, the overall throughput of the process is hindered by the fouling that occurs on and/or within the filtration media over short operating periods. To improve the throughput from fast pyrolysis bio-oil cross-flow microfiltration, the use of offline and on-line cleaning techniques were experimentally evaluated. On-line cleaning strategies using permeate, solvent, and compressed air confirmed the reversibility of the accumulated fouling layer over a small (<10) number of cleaning cycles. The use of compressed air as a simple on-line cleaning strategy was further examined over extended operating times, including a total of 31 consecutive backflushing cycles. Compared to the reference case (no cleaning), on-line compressed air backflushing increased the overall throughput of low solids permeates by more than 100%. Ultimately, the demonstration of an on-line fouling remediation strategy for fast pyrolysis bio-oil cross-flow microfiltration increases the likelihood that it could be a viable treatment pathway for suspended solids and/or ash removal in pyrolysis liquids before end-use and/or upgrading of the biofuel.