The application of chemical operations in food processing, in which pure chemical compounds are used to modify food ingredients, often raises social concerns. One of the most frequently modified dietary substances is starch, e.g., E1401–E1404, E1412–E1414, E1420, E1422, E1440, E1442, and E1450–E1452. An alternative solution to chemical treatments seems to be the use of raw materials naturally containing substrates applied for starch modification. Heating starch with a lemon juice concentrate can be considered a novel and effective method for producing starch citrate, which is part of the so-called “green chemistry”. The modified preparations obtained as a result of potato starch esterification with natural lemon juice had a comparable degree of esterification to that of the esters produced with pure citric acid. In addition, the use of the juice doubled their resistance to amylolytic enzymes compared to the preparations made with pure acid. Replacing citric acid with lemon juice can facilitate the esterification process, and the analyzed properties of both types of modified preparations indicate that starch esters produced with pure citric acid can be successfully replaced by those produced using natural lemon juice, which may increase the social acceptance of these modified preparations.