Urbanization and agriculture growth are some of the major causes of natural ecosystems depletion and biodiversity loss. Conservation efforts can be developed through the prioritization of areas for forest conservation in order to minimize this process. Here, we establish conservation strategies based on a spatial analysis of forest fragments in an urban landscape at the transition between two important Brazilian biodiversity hotspots: Atlantic Forest and Cerrado. A high-resolution mapping of forest patches was used to quantify forest cover and to provide spatial analysis. We developed a Forest Conservation Priority Index (FCPI) derived from landscape metrics to select priority areas for forest conservation efforts. We used area, shape and proximity metrics as landscape structure indicators. Landscape metrics were classified and we attributed a rank and weights for them to calculate the FCPI. Forest covers 17% of the study area. 60% of the forest patches comprise less than one hectare, 95% less than 10 ha and only 1% more than 50 ha. The largest fragments (> 100ha) are all long and narrow. Also, fewer than half the patches are connected to others. Regions classified as high and very high priority for forest conservation are localized at greater slopes, along rivers and on private lands. Our index allowed the prioritization of forest fragments in an urban landscape, directing efforts of conservation. Creating protected areas and restoration plans are necessary for the better situation of the natural ecosystem. Land-use planning must resolve human demands and conservation of this important ecosystem.