Urban areas benefit from the ecosystem services provided by low input green roofs. However, limited substrate depth on these green roofs creates challenging conditions for plant establishment and survival, leading to industry reliance on non‐native succulents. Through a green roof and glasshouse study, we assessed the impact of simple design modifications to the green roof surface, including redistribution of substrate and addition of logs and pebble piles, on both substrate temperature and moisture content. We added seeds of 26 native species and quantified seedling density, species richness and composition over a single growing season. Overall effects of microsite heterogeneity on species diversity were assessed using species accumulation curves. The modifications altered substrate temperature and moisture. Deep substrate (10–12 cm) and the presence of surface features reduced the temperature by 14.6°C and, while surface features had mixed effects on substrate moisture on the green roof, pebble piles slowed moisture loss during a 6‐week drought in the glasshouse. Following drought conditions, seedling density and species richness were greatest, relative to seeded controls, where substrate was deep on the green roof and where pebbles were present in glasshouse modules, despite high mortality overall. Design modifications did not result in differentiation of seedling communities among different microsite types. Species accumulation curves showed no difference in species richness between aggregates of modified vs. unaltered microsites. Synthesis and applications. Redistribution of green roof substrate and the addition of logs and pebble piles altered microsite conditions and created habitat heterogeneity on a green roof. These design modifications represent a minimalist strategy to ameliorate growing conditions, improve seedling survival and decrease species loss on shallow substrate green roofs.