An image sensor may contain an array of imaging pixels arranged in rows and columns. Each column of imaging pixels may be coupled to a column line which is used to read out imaging signals from the pixels. The column line may be coupled to an analog-to-digital converter for converting analog imaging signals from the pixels to digital signals. An amplifier may be included to amplify the analog imaging signals before being converted by the analog-to-digital converter. However, amplifier gain uncertainties may lead to errors in the result of the analog-to-digital conversion when the analog imaging signals are amplified by an amplifier. To mitigate these types of errors, the reference voltage for a digital-to-analog converter in the analog-to-digital converter may also be amplified by the amplifier. By multiplying the reference voltage by the same amplifier gain as the imaging signals, uncertainties in the amplifier gain will not affect the results of the analog-to-digital conversion.