Functional groups containing heteroatoms in low oxidation states can be oxidised by trifluoroperacetic acid. Common cases include the oxidation of iodine (for example, the formation of the hypervalent iodine compound from iodobenzene mentioned earlier), nitrogen, sulfur, and selenium.
In the case of nitrogen-containing compounds, known transformations include oximes and aromatic primary amines to nitro compounds (even with electron-withdrawing substituents, for example, pentafluoroaniline to pentafluoronitrobenzene), nitrosamines to nitramines, formation of aromatic N-oxides and aromatic azine N-oxides, and conversion of nitroso compounds to nitro compounds or nitramines.  For example, a mixture of hydrogen peroxide and trifluoroperacetic acid oxidises the nitroso-substituted pyrimidine 4,6-diamino-5-nitrosopyrimidine-2-thiol to its nitro analogue while also removing the thiol moiety by oxidative hydrolytic desulfurization:
In the case of chalcogen elements, sulfide moieties (R–S–R) can be oxidised by trifluoroperacetic acid to sulfoxide (R–S(O)–R) and/or sulfone (R–S(O)–R) forms, depending on the conditions used.  In the analogous selenium system, trifluoroperacetic acid oxidation of selenoethers (R–Se–R) produces selones (R–Se(O)–R) without the formation of the related selenoxides (R–Se(O)–R) as an isolable product, a reaction which is particularly effective when the R is an aryl group.  A general approach to the formation of sulfinyl chlorides (RS(O)Cl) is the reaction of the corresponding thiol with sulfuryl chloride (). In cases where the sulfenyl chloride (RSCl) results instead, a subsequent trifluoroperacetic acid oxidation affords the desired product, as in the case of 2,2,2-trifluoro-1,1-diphenylethanethiol:
The trifluoroperacetic acid oxidation of thiophene illustrates competing pathways for reaction, with both S-oxidation and epoxidation being possible.  The major pathway initially forms the sulfoxide, but this chemical promptly undergoes a Diels-Alder-type dimerisation before any further oxidation occurs—neither thiophene-S-oxide or thiophene-S,S-dioxide are found among the products of the reaction. The dimer can then be oxidized further, converting one of the S-oxide moieties to an S,S-dioxide. In the minor reaction pathway, a Prilezhaev epoxidation results in the formation of thiophene-2,3-epoxide that rapidly rearranges to the isomer thiophene-2-one.  Trapping experiments demonstrate that this epoxide pathway is not an alternative reaction of the S-oxide intermediate, and isotopic labeling experiments demonstrate that a 1,2-hydride shift (an NIH shift) occurs and thus that a cationic intermediate is involved.  The choice of trifluoroperacetic acid preparation method is important as water suppresses the minor reaction pathway, likely because it acts as a competing base.