This study presents a cross-verification of fast ion effects on turbulence through a systematic comparison of two leading gyrokinetic codes, GENE Jenko et al (2000 Phys. Plasmas7 1904–10) and CGYRO Candy et al (2016 J. Comput. Phys.324 73–93), using L-mode plasma profiles from KSTAR for local linear and nonlinear electromagnetic simulations. The focus is on the impact of fast ions and rotation effects on energy flux, aiming to identify the similarities and differences between these codes in the context of turbulence transport research. The analysis shows consistency in linear stability results, fractional changes in energy flux, changes in the spectral distribution of energy fluxes, fluctuations and phase angle with fast ions, and zonal shearing between the codes. However, discrepancies arise in absolute thermal energy levels and rotation effects on energy transport, especially in the presence of fast ions. The study underscores the critical importance of phase angle analysis in gyrokinetic code verification, particularly when assessing fast ion effects on turbulence. Additionally, it highlights the need to examine quantities at lower levels of the primacy hierarchy, as discrepancies at lower levels can lead to divergent results at higher levels. These findings indicate the necessity for further investigation into these discrepancies and the novel phase angle structures observed, contributing to the advancement of accurate transport predictions in fusion plasmas. The near-marginality inferred in this study introduces additional challenges for precise cross-code comparisons; future research will further explore strategies to address these issues and enhance verification methodologies.