The effect of nano‐Ni catalyst post‐synthetic Zr‐modification on hydrogenation reaction of 6‐methyl‐5‐hepten‐2‐one was investigated in a fixed bed continuous‐flow micro‐reactor to produce fine chemicals. The catalytic performance revealed that Zr‐doping achieved by surface organometallic chemistry approach modifies the natural aptitude of nickel to hydrogenate C=C bond, since the addition of small quantities of zirconium significantly increased the amount of unsaturated and saturated alcohols formed in 6‐methyl‐5‐hepten‐2‐one hydrogenation. Quantum chemical calculations revealed a stronger interaction between Zr←O=C that promotes the formation of C=C semihydrogenation product and enhances the probability of complete hydrogenation. The on‐the‐fly strategy presented herein enables for rapid optimization and understanding of catalytic processes.