<p>The Metropolitan Area of São Paulo (MASP), located within Brazil’s Atlantic Forest, a global biodiversity hotspot, preserves forest remnants that are essential for biodiversity and ecosystem services. However, intense urbanization and air pollution increase pressures on these remnants, demanding continuous monitoring to guide conservation strategies. UAV-based multispectral remote sensing, particularly the Normalized Difference Vegetation Index (NDVI), enables fine-scale vegetation evaluation, supporting urban forest management. This study applied UAV-based multispectral remote sensing to monitor three urban forests within the MASP—Fontes do Ipiranga State Park (PEFI), Instituto de Biociências Forest Reserve (RFIB), and Morro Grande Forest Reserve (RFMG)—over 1 year. Monthly UAV flights acquired multispectral imagery, and NDVI was used to evaluate canopy greenness. Linear regression models assessed the influence of seasonality, air temperature, and precipitation, while non-parametric tests evaluated seasonal and inter-fragment differences. NDVI showed pronounced seasonal variation across all sites, with higher values during the rainy season. Site-specific models revealed contrasting climatic sensitivities: seasonality explained a large proportion of NDVI variability at PEFI (<i>R</i>² = 0.84) and RFMG (<i>R</i>² = 0.72), whereas RFIB showed weaker climatic control (<i>R</i>² = 0.45). At PEFI, NDVI was most strongly associated with temperature (<i>R</i>² = 0.66), potentially reflecting urban heat island effects. RFMG exhibited consistently lower NDVI, likely related to sandier soils and reduced water retention, while RFIB showed high NDVI values but weaker climate coupling, suggesting stronger anthropogenic and structural influences. These results demonstrate that NDVI effectively captures spatio-temporal vegetation dynamics in tropical urban forests.</p>