Pipe organs are complex timbral synthesisers in an early acousmatic setting, which have always accompanied the evolution of music and technology. The most recent development is digital augmentation: the organ sound is captured, transformed and then played back in real time. The present augmented organ project relies on three main aesthetic principles: microphony, fusion and instrumentality. Microphony means that sounds are captured inside the organ case, close to the pipes. Real-time audio effects are then applied to the internal sounds before they are played back over loudspeakers; the transformed sounds interact with the original sounds of the pipe organ. The fusion principle exploits the blending effect of the acoustic space surrounding the instrument; the room response transforms the sounds of many single-sound sources into a consistent and organ-typical soundscape at the listener’s position. The instrumentality principle restricts electroacoustic processing to organ sounds only, excluding non-organ sound sources or samples. This article proposes a taxonomy of musical effects. It discusses aesthetic questions concerning the perceptual fusion of acoustic and electronic sources. Both extended playing techniques and digital audio can create musical gestures that conjoin the heterogeneous sonic worlds of pipe organs and electronics. This results in a paradoxical listening experience of unity in the diversity: the music is at the same time electroacoustic and instrumental.