In the field of new psychophysics, the magnitude estimation procedure is one of the most frequently used methods. It requires participants to assess the intensity of a stimulus in relation to a reference. In three studies, we examined whether difficulties of thinking in ratios influence participants’ intensity perceptions. In Study 1, a standard magnitude estimation procedure was compared to an adapted procedure in which the numerical response dimension was reversed so that smaller (larger) numbers indicated brighter (darker) stimuli. In Study 2, participants first had to indicate whether a stimulus was brighter or darker compared to the reference, and only afterwards they estimated the magnitude of this difference, always using ratings above the reference to indicate their perception. In Study 3, we applied the same procedure as in Study 2 to a different physical dimension (red saturation). Results from Study 1 (N = 20) showed that participants in the reversal condition used more (less) extreme ratings for brighter (darker) stimuli compared to the standard condition. Data from the unidirectional method applied in Study 2 (N = 34) suggested a linear psychophysical function for brightness perception. Similar results were found for red saturation in Study 3 (N = 36) with a less curved power function describing the association between objective red saturation and perceived redness perception. We conclude that the typical power functions that emerge when using a standard magnitude estimation procedure might be biased due to difficulties experienced by participants to think in ratios.