In a Josephson junction involving multiband superconductors, competition between interband and interjunction Josephson couplings gives rise to frustration and spatial disjunction of superfluid densities among superconducting condensates1–7. Such frustrated coupling manifests as the quantum interference of Josephson currents from different tunnelling channels and becomes tunable if channel transparency can be varied5–8. To explore these unconventional effects in the prototypical s±-wave superconductor FeSe (ref. 9), we use atomic-resolution scanned Josephson tunnelling microscopy10–13 for condensate-resolved imaging and junction tuning—capabilities unattainable in macroscopic Josephson devices with fixed characteristics. We quantitatively demonstrate frustrated Josephson tunnelling by examining two tunnelling inequalities. The relative transparency of two parallel tunnelling pathways is found tunable, revealing a tendency towards a 0–π transition with decreasing scanned Josephson tunnelling microscopy junction resistance. The simultaneous visualization of both superconducting condensates reveals anticorrelated superfluid modulations, highlighting the role of interband scattering. Our study establishes scanned Josephson tunnelling microscopy as a powerful tool enabling new research frontiers of multicondensate superconductivity.