Cholesterol blood levels in low-density lipoproteins (LDLs) are a key parameter for assessing the risk of cardiovascular diseases. Direct quantification of LDL cholesterol at the point of care would be possible if all other lipoproteins, particularly the high-density lipoproteins (HDLs), could be removed prior to measurement. Here, we investigated whether a molecularly imprinted membrane (MIM) could be used for the solid-phase affinity extraction (SPAE) of HDL in a paper-based lateral flow test. Samples traveled by capillarity through the MIM before reaching a detection zone where LDL cholesterol was quantified enzymatically. MIMs were produced by impregnation of the membrane with a dispersion of molecularly imprinted polymers (MIPs) selective for HDL. MIPs were synthesized using precipitation polymerization and exhibited good selectivity for HDL compared with LDL and an uptake capacity of 5.0–7.0 µg of HDL-C/mg of MIP. The MIM enabled the removal of HDL with an efficiency of typically 68%. However, quantification of LDL cholesterol suffered from strong non-specific binding of LDL, likely due to its inherent colloidal instability. Overall, our results highlight the challenges associated with SPAE of colloidal particles. Furthermore, our study demonstrates a novel, efficient, and potentially generic modality to integrate SPAE into paper-based POC diagnostic tests.