Organic–inorganic metal halide perovskites have led to remarkable advancements in emerging photovoltaics with power conversion efficiencies (PCEs) already achieving 20%. In addition to solar cells, these perovskites also show applicability for lasing and LED applications. Here, we control perovskite crystal domain size and microstructure by guiding the growth through a highly ordered metal oxide honeycomb structure, which we form via colloidal monolayer lithography. The organic–inorganic perovskite material fills the holes of the honeycomb remarkably well leading to fully controlled domain size with tuneable film thickness. The honeycomb region is predominantly transparent, whereas the perovskite crystals within the honeycomb are strongly absorbing. We fabricate semi-transparent perovskite solar cells to demonstrate the feasibility of this structuring, which leads to enhanced open-circuit voltage and fill factor in comparison to unstructured partially dewet perovskite thin films. We achieve power conversion efficiencies of up to 9.5% with an average visible transmittance through the active layer of around 37%. The controlled microscopic morphology of perovskite films opens up a wide range of possible investigations, from charge transport optimization to optical enhancements and photonic structuring for photovoltaic, light emitting and lasing devices.