Purpose: Quantitative fundus autofluorescence (QAF) currently deploys an age-based score to correct for lens opacification. However, in elderly people, lens opacification varies strongly between individuals of similar age, and innate lens autofluorescence is not included in the current correction formula. Our goal was to develop and compare an individualized formula. Methods: One hundred thirty participants were examined cross-sectionally, and a subset of 30 participants received additional multimodal imaging 2-week post-cataract-surgery. Imaging included the Scheimpflug principle, anterior chamber optical coherence tomography (AC-OCT), lens quantitative autofluorescence (LQAF), and retinal QAF imaging. Among the subset, least absolute shrinkage and selection operator regression and backward selection was implemented to determine which lens score best predicts the QAF value after lens extraction. Subsequently, a spline mixed model was applied to the whole cohort to quantify the influence of LQAF and Scheimpflug on QAF. Results: Age and LQAF measurements were found to be the most relevant variables, whereas AC-OCT measurements and Scheimpflug were eliminated by backward selection. Both an increase in Scheimpflug and LQAF values were associated with a decrease in QAF. The prediction error of the spline model (mean absolute error [MAE] $±$ standard deviation) of 32.2 $±$ 23.4 (QAF a.u.) was markedly lower compared to the current age-based formula MAE of 96.1 $±$ 93.5. Both smooth terms, LQAF (P < 0.01) and Scheimpflug (P < 0.001), were significant for the spline mixed model. Conclusions: LQAF imaging proved to be the most predictive for the impact of the natural lens on QAF imaging. The application of lens scores in the clinic could improve the accuracy of QAF imaging interpretation and might allow including aged patients in future QAF studies.