In this work, nanosphere lithography was integrated with standard microfabrication for the wafer-scale fabrication of silicon nitride (SiN) membranes with arrays of submicrometer holes. A monolayer of polystyrene (PS) beads with a mean diameter of 428 or 535 nm was spin coated onto the front side of a (100)-silicon wafer double-side coated with 100 nm of low-stress SiN. The size of the deposited PS beads was reduced by oxygen plasma reactive ion etching. This allowed to tune the hole size in the released SiN membrane while maintaining the hole array periodicity. Using the size-reduced PS beads as a lift-off template in a standard nanosphere lithography lift-off procedure, a 20 nm thick chromium hole etch mask was realized. This hole mask was patterned by UV photolithography, thus allowing for the local dry-etching of holes into the SiN layer. The holey areas were released from the backside in a combined Si dry- and wet-etch process. During the final wet etch, the wafer front side was protected with a KOH-resistant polymeric coating (ProTEK®). In this way, holey SiN membranes with side lengths ranging from 400 um up to 2.4 mm were fabricated. Preliminary application specific experiments show the membranes’ suitability for microfiltration and stencil applications.