Flexible conductive materials have greatly promoted the rapid development of intelligent and wearable textiles. This article reports the design of flexible polypyrrole/bacterial cellulose (PPy/BC) conductive nanocomposites by in situ chemical polymerization. Box-Behnken response surface methodology has been applied to optimize the process. The effects of the pyrrole amount, the molar ratio of HCl to pyrrole and polymerization time on conductivity were investigated. A flexible PPy/BC nanocomposite was obtained with an outstanding electrical conductivity as high as 7.34 S cm−1. Morphological, thermal stability and electrochemical properties of the nanocomposite were also studied. The flexible PPy/BC composite with a core-sheath structure exhibited higher thermal stability than pure cellulose, possessed a high areal capacitance of 1001.26 mF cm−2 at the discharge current density of 1 mA cm−2, but its cycling stability could be further improved. The findings of this research demonstrate that the response surface methodology is one of the most effective approaches for optimizing the conditions of synthesis. It also indicates that the PPy/BC composite is a promising material for applications in intelligent and wearable textiles.