In this paper we report the influence of biopolymer folding on nanoparticle spatial distribution in two typical bio-nanocomposite hydrogels. These systems consist of negatively charged nanosized fillers (polyoxotungstate clusters and silica particles, 2.2 nm and 23.0 nm in diameter, respectively) dispersed at low volume fractions in a positively charged gelatin hydrogel. The filler state of dispersion is investigated during triple helix folding by combining small-angle neutron scattering (SANS) and polarimetry experiments. Neutron contrast matching/polarimetry correlations indicate that the nanoparticle spatial distribution is clearly modified during triple helix folding for the two systems. In the first case, polyoxotungstate clusters are initially arranged in small finite size aggregates that grow with increasing triple helix rate: ΔRG ≈ +150% and ΔI(q → 0) ≈ +250% for Δ[helix] ≈ +40%. In the second case, silica particles initially form a connected network that undergoes a significant densification through gelatin conformational transition. In the two cases, the kinetics of triple helix folding is only slightly affected by the presence of the nanoparticles and their state of dispersion. In our experimental conditions, these two processes are almost thermo-reversible following triple helix unfolding.