In the present work, anthocyanin (ACN) hybrid nanopigments were synthetized by using a natural pomegranate dye (PD) and calcined hydrotalcite (HT) and montmorillonite (MMT) nanoclays. A wide colour gamut was obtained with MMT-based nanopigments ranging from reddish to bluish hues caused by structural transformations of ACNs at different pH values. However, a buffer effect was observed with HT obtaining samples a similar final colour regardless of the synthesis conditions. Nanopigments added with a biomordant extracted from pomegranate peels showed a different colour compared to the incorporation of a commercial mordant due to the intrinsic colouring properties of the pomegranate bioadditive. The developed nanopigments were incorporated at 7 wt% loading to produce novel polyester-based bionanocomposites which were characterized in terms of thermal, mechanical and colour properties. The encapsulation of PD into the nanoclays improved its thermal stability, in particular for MMT-based nanopigments. The pH changes observed during the nanofillers synthesis affected the final colour of the MMT-based nanocomposites, inducing a general increase in ΔE* and a decrease in gloss values. Slight improvements were obtained in terms of elastic modulus for MMT-based polymer samples confirming the applicability of the developed bionanocomposites as colouring and reinforcement materials. A very similar environmental profile was obtained for MMT and HT-based nanofillers showing MMT-based nanopigments a slightly better general behaviour. The results of the LCA study evidenced the suitability of the processes used in this work to the circular bioeconomy approach through sustainable food waste management and the production of bioplastics using waste substrates. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.