L-Pipecolic Acid (L-PA) is a valuable building block for the synthesis of pharmaceuticals such as anesthetics and immunosuppressants. Thus, more efficient and greener strategies are desired for its production. Herein, we have applied a previously engineered variant of the Lysine Cyclodeaminase from Streptomyces pristinaespiralis (e-SpLCD) for the bioconversion of L-Lysine into L-PA. The reaction can be performed by the free e-SpLCD reaching full conversion to 50 mM L-PA. From a biotechnological perspective, the process scale-up has been trialed in a SpinChem® reactor, albeit with lower conversion yields. To further enhance the biocatalyst stability, we present a detailed study of the e-SpLCD immobilization on microparticles. This enabled the integration of the immobilized biocatalyst into a packed-bed reactor for the continuous flow synthesis of L-PA. The full conversion was achieved in 90 min, maintaining also high operational stability. Remarkably, the addition of exogenous cofactor was not needed for the flow reaction, although the long-term operational stability was improved by the addition of NAD+.