High quality, ultra-thin single crystal diamond (SCD) membranes that have a thickness in the sub-micron range are of extreme importance as a materials platform for photonics, quantum sensing, nano/micro electro-mechanical systems (N/MEMS) and other diverse applications. However, the scalable fabrication of such thin SCD membranes is a challenging process. In this paper, we demonstrate a new method which enables high quality, large size (∼4 × 4 mm) and low surface roughness, low strain, ultra-thin SCD membranes which can be fabricated without deformations such as breakage, bowing or bending. These membranes are easy to handle making them particularly suitable for fabrication of optical and mechanical devices. We demonstrate arrays of single crystal diamond membrane windows (SCDMW), each up to 1 × 1 mm in dimension and as thin as ∼300 nm, supported by a diamond frame as thick as ∼150 μm. The fabrication method is robust, reproducible, scalable and cost effective. Microwave plasma chemical vapour deposition is used for in situ creation of single nitrogen-vacancy (NV) centers into the thin SCDMW. We have also developed SCD drum head mechanical resonator composed of our fully clamped and freely suspended membranes.