Soundscape research has acquired a paramount role in biodiversity conservation as it may provide timely and reliable information about the ecological integrity. The relationship between soundscape complexity and ecological integrity in highly biodiverse environments, as well as the factors affecting this relationship require a thorough understanding. We determined how the soundscape relates to the landscape ecological integrity at different spatial and temporal scales in a montane forest in the northern Andes of Colombia. Between May–July 2018 we obtained acoustic recordings from 31 sampling sites in the protected area of a hydropower plant, and estimated nine acoustic indices and an ecological integrity index (EII) derived from fragmentation, connectivity, and habitat quality. Five of the acoustic indices, linked to the evenness of the acoustic signals and levels of the biophonic signals, were associated with changes in the EII and indicated the presence of more even, saturated, and acoustically rich soundscapes in sites with higher integrity. Relationships between acoustic indices and the EII were stronger at a smaller spatial scale (100 m) and responded to daily variation of the soundscape, with the strongest associations occurring mainly from sunrise to noon. We show that acoustic indices measuring the evenness of the acoustic activity distribution and the number of frequency peaks reliably reflect the changes in the ecological integrity, and can be integrated with remote sensing as a tool for landscape management. Our results highlight the soundscape analysis as a feasible approach for the monitoring and conservation planning of acoustically unknown and threatened Andean landscapes.