Multivalent manganese‐based Prussian blue analogues (Mn‐PBA) possess multi‐electron transfer characteristics and exhibit unique properties for achieving high energy density in ammonium ion batteries (AIBs). However, the irreversible structural collapse and sluggish ionic diffusion kinetics result in inferior rate capability and undesirable lifespan. Herein, guided by theoretical calculations, a series of ultrafine Mn‐PBA@ conductive polymers core–shell composites through an in situ polymerization and encapsulation strategy are synthesized to solve the above existing issues for Mn‐PBA. Among various designed conductive polymers (including the poly‐pyrrole (ppy), polyaniline, and poly(3,4‐ethylenedioxythiophene)) coated on Mn‐PBA, the Mn‐PBA@ppy shows the strongest adsorption for ammonium ions and the highest manganese atom removal energy barrier. Acting as the cathode of AIBs, the designed Mn‐PBA@ppy exhibits a remarkable high capacity of 72 mAh g−1, a super‐stable discharge platform of 0.81 V, and excellent cycling stability of 94% retention for over 300 cycles (0.1 A g−1) with an ultrahigh NH4+ diffusion coefficient of ≈1.38 × 10−8 cm−2 s−1. This work offers an in situ polymer encapsulation approach to simultaneously enhance the ammonium ion diffusion kinetics and structural stability. More importantly, this organic/inorganic interfacial design can promote the development of cathode materials with rapid diffusion kinetics and excellent cyclic stability.