A system and method for increasing the speed of individualizing amplifier gain optimization in implantable medical devices. A variable amplifier gain is initially set at a relatively high level such that the amplifier experiences at least intervals of saturation. A saturation indicator is determined which is indicative of the relative degree of saturation. The gain is then adjusted as a function of the saturation indicator. Relative larger degrees of saturation result in more aggressive gain adjustment. This increases the speed of adjustment with reduced likelihood of loss of sensing. In one implementation, one or more discrete amplifier gain adjustment steps are made in a single adjustment to effectively skip over intermediate adjustments. In another implementation, an estimate is made of a signal peak during a saturating interval. The gain is adjusted directly based on the estimated peak with appropriate sensing safety margins. The method can be implemented with a system including a programmer in communication with an implantable device.