The study examines supersonic square jets in a twin nozzle configuration with the aim of identifying and characterising emergent instability modes during overexpanded operation. Unlike screeching rectangular jets that undergo strong fluctuations normal to the wider jet dimension, the equilateral nature of the exit geometry in square nozzles leads to multiple instability states dictated by shock–turbulence interactions and nozzle operating conditions. Furthermore, strong coupling modes between the jets were identified that led to either phase locked or out of phase interactions of the inner shear layers. Results from experimental studies were examined using spatial and temporal decomposition techniques based on spectral methods to identify the resultants from triadic shock–turbulence interactions. The primary instability mode across both operating conditions were driven by optimal interactions while the harmonics were found to be associated with the suboptimal shock–turbulence interactions.