Many applications of plant genetic engineering require tight control of transgene expression to a particular organ, tissue or developmental stage, particularly when off-target expression causes deleterious effects. Most studies have relied on tissue-specific and developmentally regulated promoters to confer the desired transgene expression pattern via transcriptional control. However, the process to identify promoters conferring required expression patterns is slow and expensive, with no certainty of success. Therefore, we investigated the practicality of post-transcriptional control of transgene expression patterns in plants, triggered by binding of endogenous small RNA sequences. Target sequences of several small RNAs, inserted 3′ of a luciferase reporter, altered transgene expression in patterns consistent with developmental abundance of the corresponding small RNAs in sugarcane. Incorporating the target sequences of miR167 or a leaf-specific small RNA selectively reduced reporter expression in leaves by more than 90 % on average, whereas incorporating the miR160-3p target sequence selectively reduced reporter expression in roots by 75 % on average across immature transgenic lines. We anticipate that the strategy should be broadly applicable in plants.