A handheld micro-electro-mechanical system (MEMS) based spectrometer working in the near infrared region (NIR) (1600-2400nm) was evaluated for in-situ and non-destructive prediction of main fatty acids in Iberian pig (IP) carcasses. 110 IP carcasses were measured. Performance of the instrument was compared with at-line high-resolution NIRS monochromators working in two analysis modes: melted fat samples (transflectance cups) and intact adipose tissues (interactance fiber optic). Standard Error of Prediction (SEP) values obtained on the MEMS-NIRS device were: 0.68% (stearic), 1.30% (oleic), 0.55% (linoleic) and 1% (palmitic), explaining a variability of 83%, 84%, 81% and 78%, respectively. As expected, this represented a loss of predictive capability in comparison to at-line models, even with the same spectral characteristics as on the handheld device. However, the estimated total errors were at the same level for gas chromatography and NIRS analysis. This indicates that the MEMS-NIRS in-situ analysis of each individual carcass provides a cost-effective and real-time quality control system with suitable accuracy.