For analysis of weak π–π complexes proton-nuclear magnetic resonance (proton-NMR) simultaneously provides information of stacking configurations and association constants $$\left( K \right)$$ K However, an apparent issue for this approach is inconsistent/impossible constant estimation which often leads to unreasonable interpretation for π–π complexation. Whether or not this proton-dependent constant variation could be attributed to simple experimental uncertainties or to more sophisticated additional unspecific shielding effects (AUS effects) was addressed by means of hypothesis tests using a robust bootstrap technique in this report. Our analysis shows the significance of AUS effects on such variation in constant estimation. A following study using numeric simulation further reveals the variation patterns induced by AUS effects and concludes that the largest $$K$$ K among the obtained $$K$$ K estimates of a complex is considered as the best estimate of $$K$$ K due to minimum deviation from the true value of K and the multiple $$K$$ K estimates of a π–π complex could provide preferable inferences for complex geometries.