Nanoscale photoisomerisation in photochromic crystals is promising for nanoscale optoelectronic applications. To further understand this phenomenon and address fundamental difficulties in measuring photoisomerisation at the nanoscale, we used scanning tunnelling spectroscopy (STS) to measure the changes in the electronic properties of the microcrystals that correspond to the photoisomerisation state. The results showed reversible changes in the electronic properties of the crystals in response to photoisomerisation between the coloured (closed ring) and decoloured (open ring) states. Furthermore, the measured tunnel current fluctuation increased as the crystal was uniformly decolourised, indicating that the measurement was sensitive to the position of the molecular-scale tunnel junction. STS measurements on the crystals visualised the relationship between the thickness of the crystals and the degree of photoisomerisation in a two-dimensional image without the use of light. Isomerisation-dependent electronic properties provide a method to visualise the photoisomerisation progress on the crystal at the nanometre scale without extra photoisomerisations and show potential as a fundamental technology for nano-optoelectronics integration.