The output of the third oscillator and/or the noise generator can also be routed to the control voltage inputs of the filter and/or oscillators. The amount of pitch or filter modulation thus realized is controlled by the modulation wheel, which is the right one of the two plastic disks located to the left of the keyboard. In this way the third oscillator is frequently used as a low-frequency oscillator to control pitch.

The Minimoog can be controlled using its in-built, 44-note keyboard, which is equipped with modulation and pitch-bend wheels or by feeding in an external one-volt-per-octave pitch-control voltage and triggering the envelope generators with an inverted trigger. External pitch control does not pass through the glide circuit, nor is presented to the VCF tracking switches and thus, the external inputs were not designed for external keyboard control. The lowest note played on the keyboard determines the pitch, a condition that is referred to as low-note priority. The envelope generators do not retrigger unless all notes are lifted before the next note is played, an important characteristic which allows phrasing. The modulation and pitch-bending wheels were an innovation that many instrumentalists found to be extremely playable. The pitch-bend wheel is on the left of the modulation wheel. It is normally kept in the centered position. It is not spring-loaded; the player must return it to the centered position to play in tune. There is a delicate detent mechanism to help the player find the center position tactually. In sharp contrast to later synthesizers that also have pitch-bend wheels, there is no "dead band" near the center of the wheel's travel; the wheel produces minute changes in pitch no matter how slightly it is moved in either direction. The wheel can therefore be used to introduce slight vibrato or nuance, as well as accurate pitch changes. However, Moog later recommended adding a deadband mod and published this mod in their factory service notes.

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