Small-scale fisheries (SSF) remain a largely under-assessed and overlooked sector by governments and researchers, despite contributing approximately 50% to global fish landings and providing food and income for millions of people. The multi-species, multi-gear and data-poor nature of SSF makes implementation of traditional single-species management approaches – like catch-quotas or size limits – particularly challenging and insufficient. A more holistic approach is thus required, which demands assessment of ecological impacts. Here we carried out an estimation of selected ecological indicators of the impact of fisheries (mean length, maximum body size, mean trophic level, trophic and spatial guilds, threatened species and landed by-catch) based on the nominal catch of different gears in three representative SSF along the Colombian Pacific using landings data collected in multiple years (2011–2017). Results showed that taxonomic, size-based, functional and conservation features of the nominal catch vary greatly with geographical location and gear type used. Overall, handlines and longlines tend to select larger sizes and higher trophic levels than nets, but they also catch a higher proportion of intrinsically vulnerable species and species of conservation concern. This challenges the idea that more selective gears have overall lower ecological impacts. In contrast, nets target a wider size range – although focusing on small or medium sized fish – and include a higher diversity of trophic and spatial guilds, which could arguably be considered a more “balanced harvest” type of fishing that retains ecosystem structure and functionality. Bottom trawls, though, exhibited a relatively high percentage of landed by-catch, an undesirable feature for any fisheries in terms of sustainability. We propose that the assessment of a suite of ecological indicators, like those implemented here, should be included as part of periodic evaluations of multi-gear and multi-species SSF in tropical coastal areas, as a practical step toward ecosystem-based fisheries management.