Grapheme-color synesthesia is a condition where the perception of graphemes consistently and automatically evokes an experience of non-physical color. Many have studied how synesthesia affects the processing of achromatic graphemes, but less is known about the synesthetic processing of physically colored graphemes. Here, we investigated how the visual processing of colored letters is affected by the congruence or incongruence of synesthetic grapheme-color associations. We briefly presented graphemes (10–150 ms) to 9 grapheme-color synesthetes and to 9 control observers. Their task was to report as many letters (targets) as possible, while ignoring digit (distractors). Graphemes were either congruently or incongruently colored with the synesthetes’ reported grapheme-color association. A mathematical model, based on Bundesen’s (1990) Theory of Visual Attention (TVA), was fitted to each observer’s data, allowing us to estimate discrete components of visual attention. The models suggested that the synesthetes processed congruent letters faster than incongruent ones, and that they were able to retain more congruent letters in visual short-term memory, while the control group’s model parameters were not significantly affected by congruence. The increase in processing speed, when synesthetes process congruent letters, suggests that synesthesia affects the processing of letters at a perceptual level. To account for the benefit in processing speed, we propose that synesthetic associations become integrated into the categories of graphemes, and that letter colors are considered as evidence for making certain perceptual categorizations in the visual system. We also propose that enhanced visual short-term memory capacity for congruently colored graphemes can be explained by the synesthetes’ expertise regarding their specific grapheme-color associations.