Hypothermic storage of boar semen may allow antibiotic‐free semen preservation but is limited due to chilling sensitivity of boar spermatozoa. Progress in this area requires sensitive tools to detect chilling injury. Therefore, multiparameter flow cytometry panels were evaluated to ascertain whether they are useful tools for identifying sublethal damage of sperm function at a single cell level, thus considering the high intrinsic sperm heterogeneity in a sample. The first fluorochrome panel consisted of Hoechst 33342 to identify DNA‐containing events, Yo‐Pro 1 to detect viability, merocyanine 540 to describe membrane fluidity, and PNA‐Alexa Fluor™ 647 to identify acrosomic integrity. The second fluorochrome panel consisted of SiR700‐DNA to identify DNA‐containing events, JC‐1 to characterize the mitochondrial transmembrane potential (MMP), and Calbryte 630 to assess the intracellular calcium level. Extended boar semen was stored either at 17°C (control) or 5°C (chilled). It is shown that chilling increased membrane fluidity in the viable (Yo‐Pro 1 negative) sperm population at 24 h (p < 0.05). At 144 h, the viable, acrosomic intact sperm population with low membrane fluidity was similar for both storage temperatures. Moreover, chilling reduced the main sperm population with high MMP, medium fluorescence for JC‐1 monomer and low intracellular calcium level (p < 0.05). However, after in vitro sperm capacitation, this population did not differ between the two storage temperatures. Exemplary computational data visualization in t‐distributed stochastic neighbor embedding (t‐SNE) maps and moving radar plots revealed similar subpopulations as identified by three‐dimensional stacked bar charts. In conclusion, sperm surviving an initial chilling injury withstand long‐term storage and respond in a similar manner to capacitation conditions as sperm stored conventionally at 17°C. Multicolor flow cytometry is a valuable tool for detecting chilling‐induced alterations of cell function in sperm subpopulations.