This research aimed to assess carbon (C) stocks (living biomass, soil and detritus) in silvopastoral systems (SPS), the C density in living biomass (CLB) at the farm level, technological adoption and milk yields in an integrated fashion in small dairy farms in the Andean-Amazon region of Colombia. Technological adoption was assessed on a scale of 0 to 100% across 26 points. Milk yields from the top 10% highest-yielding farms were used for gap analysis. The lactation period and weaning age were considered as herd management variables. The study included 30 farms classified as high, medium or low SPS coverage. The average farm size was 9.1 ± 0.8 ha−1 where live fences (LF) and woodlots (WL) were the main SPS. The total C were 152.0 ± 13.8 Mg·ha-1, 152.2 ± 10.3 Mg·ha-1, and 73.2 ± 4.4 Mg·ha-1 in WL, LF and pastures. Farms with high SPS coverage (10.8 ± 1.1%) presented a CLB density of 8.6 ± 2.0 Mg·ha−1, 3.4 and 43 times higher than those with medium and low coverage, respectively. Average milk yield was 3190.1 ± 237.5 kg fat and protein-corrected milk (FPCM) cow−1 yr⁻1, with the top 10% of farms having 6056.7 kg·FPCM·cow−1 yr⁻1. Farms with low SPS coverage had the smallest yield gap (1221.4 ± 290 kg·FPCM·cow−1 yr⁻1) but also a lower average yield (2883.0 ± 290 kg·FPCM·cow⁻1·yr⁻1). The farms averaged 48.9 ± 2.1% in the technological adoption level, 271.5 ± 8.4 days of lactation period, and 129.3 ± 17.8 days of weaning age, with no significant differences across SPS levels. An integrated approach to jointly increase technology adoption, herd management, and the enhancement of SPS coverage at the farm level can reduce the yield gap while enhancing C stocks.