The Brazilian Atlantic Forest (AF) covers 13% of Brazil but retains only 26% of its original forest area. Utilizing a Morphological Spatial Pattern Analysis (MSPA), we generated 30-m spatial resolution fragmentation maps for old-growth and secondary forests across the AF. We quantified landscape fragmentation patterns and carbon (C) dynamics over 35 years using MapBiomas data between the years 1985 and 2020. We found that from 1985 to 2020 the forest suffered continuous fragmentation, losing core (nuclei forest fragments) and bridge (areas that connect different core areas) components of the landscape. About 87.5% (290,468.4 km²) of the remaining forest lacked core areas, with bridges (38.0%) and islets (small, isolated fragments) (35.4%) being predominant. Secondary forests (1986-2020) accounted for 99,450.5 km² and played a significant role in fragmentation pattern, constituting 44.9% of the areas affected by edge effects (perforation, edge, bridge, and loop), 53.7% of islets, and comprising only 1.4% of core forest. Additionally, regeneration by secondary forests contributed to all fragmentation classes in 2020. Even with the regrowth of forests, the total forested area in the biome did not increase between 1985 and 2020. Deforestation emissions reached 818 Tg CO2, closely paralleled by edge effects emissions at 810 Tg CO2, highlighting a remarkable parity in C emissions between the two processes. Despite slow changes, AF biome continues to lose its C stocks. We estimated that around 1.96 million hectares (19,600 km2) of regenerated forest would be required to offset the historical C emissions over the analyzed period. Hence, MSPA can support landscape monitoring, optimizing natural or active forest regeneration to reduce fragmentation and enhance C stocks. Our study's findings are critical for guiding land-use policies focusing on minimizing emissions, promoting forest regrowth, and monitoring its permanence. This work offers biome scale, spatially explicit information, critical for AF conservation and management.