The Schwartz (J Finance 52(3):923–973, 1997) two factor model serves as a benchmark for pricing commodity contracts, futures and options. It is normally calibrated to fit the term-structure of a range of future contracts with varying maturities. In this paper, we investigate the effects on parameter estimates, if the model is fitted to prices of options, with varying maturities and strikes instead of futures, as is commonly done. The use of option prices rather than futures in the calibration leads to non-linearities, which the standard Kalman filter approach is unable to cope with. To overcome these issues, we use the extended Kalman Filter. We find that some parameters sensitively depend on the choice of strikes of the corresponding options, and are different from those estimates obtained from using futures prices. This effect is analogue to varying implied volatilities in the Black–Scholes model. This realization is important, as the use of ill-fitted models for pricing options in the Schwartz (1997) framework may cause traders to bear serious financial losses.