Maintaining the protein activity and stability under acidic conditions is important in bioengineering and biomedical applications. Polyelectrolyte conjugation as a means of stabilizing proteins has received much recent attention. Retention of protein activity, and especially, improvement of protein stability by minimizing the number of polymer chains in the conjugate, as well as by choosing the optimal site for conjugation, is critical in practical applications. In this research, the cationic polyelectrolyte poly(2-(dimethylamino)ethyl methacrylate) (pDMAEMA) was conjugated to the inorganic pyrophosphatase (PPase) site specifically. Conjugation of pDMAEMA to the specific site N124 on the protein surface led to a significant increase in activity at acidic pH. At pH 4.0, the activity of the pDMAEMA-conjugated protein was increased 3-fold relative to the unconjugated one. Dynamic light scattering (DLS) measurements showed that the aggregation state of the protein depended on the polymer charge as the pH was varied. Protein aggregation at low pH was prevented by pDMAEMA conjugation, resulting in an increase in protein stability under acidic conditions. The conjugate retained 60% of its initial activity after 4 h at pH 4.0, whereas the unconjugated protein lost 40% of its initial activity within 15 min at this pH. These results suggest an approach for preserving the protein activity and stability at low pH based on site-specific polyelectrolyte conjugation to the protein surface, thereby providing a new strategy for expanding the use of proteins in an acidic environment.