Olive tree cultivation is currently a dominant agriculture activity in the Mediterranean basin, where the increasing impact of climate change coupled with the inefficient management of olive groves is negatively affecting olive oil production and quality in some marginal areas. In this context, satellite imagery may help to monitor crop growth under different environmental conditions, thus providing useful information for optimizing olive grove management and final production. However, the spatial resolution of freely-available satellite products is not yet adequate to estimate plant biophysical parameters in complex agroecosystems such as olive groves, where both olive trees and grass cover contribute to the vegetation indices (VIs) signal at pixel scale. The aim of this study is therefore to test a disentangling procedure to partition the VIs signal among the different components of the agroecosystem to use this information for the monitoring of olive growth processes during the season. Specifically, five VIs (GEMI, MCARI2, NDVI, OSAVI, MCARI2/OSAVI) as recorded by Sentinel-2 at a spatial resolution of 10 m over five olive groves in the Montalbano area (Tuscany, Central Italy), were tested as a proxy for olive tree intercepted radiation. The olive tree volume per pixel was initially used to linearly rescale the VIs signal into the relevant value for the grass cover and olive trees. The models, describing the relationship between rescaled VIs and observed fraction of Photosynthetically Active Radiation (fPAR), were fitted and then validated against independent datasets. While in the calibration phase, a greater robustness at predicting fPAR was obtained using NDVI (r = 0.96 and RRMSE = 9.86), the validation results demonstrating that GEMI and MCARI2/OSAVI provided the highest performances (GEMI: r = 0.89 and RRMSE = 21.71; MCARI2/OSAVI: r = 0.87 and RRMSE = 25.50), in contrast to MCARI2 that provided the lowest (r = 0.67 and RRMSE = 36.78). These results may be related to the VIs’ intrinsic features (e.g., lower sensitivity to atmosphere and background effects), which make some of these indices, compared to others, less sensitive to saturation effects by improving fPAR estimation (e.g., GEMI vs. NDVI). On this basis, this study evidenced the need to improve the current methodologies to reduce inter-row effects and select appropriate VIs for fPAR estimation, especially in complex agroecosystems where inter-row grass growth may affect remote sensed-derived VIs signal at an inadequate pixel resolution.