Many per- and polyfluoroalkyl substances (PFAS) have either carboxylic acid or sulfonic acid as their polar functional group. Studies to date have consistently shown that accumulation of short-chain PFAS containing sulfonic acid in fruits is much more limited than those with carboxylic acid, but the underlying mechanisms are not known. In this study, using the functional group as the sole variable, the concentrations of perfluoropentanoic acid (PFPeA) and perfluorobutanesulfonic acid (PFBS) in various organs of tomato plants were monitored following different treatments to evaluate their transport patterns and identify biological barriers. Concentrations in fruits of tomato grown in nutrient solution with 0.80 μM PFAS were up to 34.83 μg/g for PFPeA, but only 0.07 μg/g for PFBS after exposure for an entire growing season. Redistribution experiments showed that 65.01% of PFPeA accumulated during the seedling stage was translocated to fruits upon maturity, whereas for PFBS, 99.99% still remained in leaves, and the level in fruits was below detection. After feeding young leaves with PFPeA or PFBS, 89.55% of PFPeA entered fruits, while PFBS was again not detected in the fruits, indicating the absence of a source-sink relationship between leaves and fruits for PFBS. Translocation out of roots appeared to be the primary bottleneck for PFBS, and preferential deposition into leaves over fruits further diminished its accumulation in fruits. Therefore, the functional group sulfonic acid impedes translocation of PFAS to fruits and plays a mitigating role in the food chain transfer of short-chain PFAS in terrestrial ecosystems and, further, human exposure.