Cortical-autonomic interactions link executive cognition and cardiovascular regulation via prefrontal-subcortical pathways. However, autonomic responses to cognitive load remain poorly explored longitudinally, specifically within-subject heart rate variability (HRV) dynamics during engagement. Thus, this work explores longitudinal cognitive-driven HRV modulation. To this aim, 13 healthy subjects (22±3 years) were enrolled for five daily sessions, each including a first resting state, memory task (MEM), a second resting state, strategy task (STR), and a last resting state; task involved fading cues over the days. Frequency-domain and nonlinear HRV features extracted from 60-s ECG segments, followed by Friedman and Wilcoxon statistical tests. Significant changes emerged during MEM and STR across days, while resting-state HRV remained stable, reflecting progressive task adaptation with increased vagally-mediated activity (p<0.01, HF and LF/HF) and altered short-term variability (p<0.01, α1). In conclusion, these findings indicate a consistent association between autonomic modulation and cognitive engagement, with progressive autonomic differentiation tracking cognitive load, thus supporting the role of HRV for monitoring sustained cognitive effort.