Cold acclimation, initiated by non-freezing low temperatures and light, is a natural strategy for increasing plant survival even at sub-zero temperatures. However, it remains unclear how the non-photochemical quenching processes, which are crucial for excessive light energy dissipation, are modulated during cold acclimation. We compared the effects of two weeks of acclimation to sub-optimal temperatures, at 10 °C (AC10) and 4 °C (AC4), with non-acclimated (NAC) Arabidopsis thaliana natural accessions grown at 21 °C, on their growth (rosette area), biochemistry (chlorophylls and epidermal flavonols), and physiology (CO2 assimilation rate, and quantum yields of photochemical and non-photochemical quenching processes). AC10 reduced rosette area in all (six) accessions, while chlorophylls and CO2 assimilation rate (Asat) decreased only in three accessions and it had no effect on maximum quantum yield (Fv/Fm). However, AC4 significantly decreased rosette area, chlorophylls, and Fv/Fm, in all accessions. Both AC10 and AC4 treatments increased the accumulation of epidermal flavonols in all accessions. In AC4 accessions, we found an increase in additional non-regulatory NPQ, Φf,d, and a decrease in the fraction of excitation energy used by PSII photochemistry, ΦPSII. A similar irradiance resulted in a marginal difference in regulatory NPQ, Φnpq, among NAC and AC10 or AC4 plants; however, AC10 plants have more energy-dependent fastest NPQ, ΦqE, whereas AC4 predominates state transition quenching, ΦqT. These variations in dissipation of absorbed light energy, when combined with reduced chlorophylls and accumulated flavonols, help to reduce the risk of photoinhibition in plants during cold periods. These findings provide new insights into how suboptimal temperature acclimation affects the regulation of NPQ molecular mechanisms in Arabidopsis thaliana natural accessions.