New affinity monolithic capillary columns of 150 μm internal diameter were prepared in situ fused glass capillary via either immobilization or encapsulation of Candida antarctica lipase B (CALB) on or within polymer monoliths, respectively. The immobilized lipase-based monoliths were prepared via copolymerization of 19.1% monomers (8.9% MMA and 10.2% GMA), 19.8% EDMA, and 61.1% porogens (54.2% formamide and 6.9% 1-propanol) w/w or 20% GMA, 20% EDMA, and 60% porogens (51.6% cyclohexanol and 8.4% 1-dodecanol) in the presence of AIBN (1%) as a radical initiator. This was followed by pumping a solution of lipase through the capillaries and rinsing with potassium phosphate buffer. On the other hand, the encapsulated lipase-based monoliths were prepared via copolymerization of 20% monomers (GMA), 20% EDMA, and 60% porogens (48% 1-propanol, 6% 1,4-butanediol) or 16.4% monomers (16% BuMA, 0.4% SPMA), 23.6% EDMA, and 60% porogens (36% 1-propanol, 18% 1,4-butanediol along with 6% lipase aqueous solution in potassium phosphate buffer. The prepared capillary columns were investigated for the enantioselective nano liquid chromatographic separation of a set of different classes of racemic pharmaceuticals, namely, α- and β-blockers, antiinflammatory drugs, antifungal drugs, dopamine antagonists, norepinephrine-dopamine reuptake inhibitors, catecholamines, sedative hypnotics, diuretics, antihistaminics, anticancer drugs, and antiarrhythmic drugs. Run-to-run repeatability was quite satisfactory. The encapsulated lipase-based capillary monolith showed better enantioselective separations of most of the investigated compounds. Baseline separation was achieved for alprenolol, atenolol, bromoglutithimide, carbuterol, chloropheneramine, cizolertine carbinol, 4-hydroxy-3-methoxymandelic acid, desmethylcizolertine, nomifensine, normetanephrine, and sulconazole under reversed phase chromatographic conditions. A speculation about the understanding of the chiral recognition mechanism of lipase-based monoliths toward the investigated pharmaceuticals is discussed.