In this paper, we have reported how the substrate holder affects the generation of diamond nucleation by biasing in microwave plasma chemical vapor deposition (MWCVD). A high density of diamond nucleation was obtained on the Si substrate when a fresh holder was used, which decreases drastically to almost no nucleation on the substrate once there is a diamond coating on the boundaries of the holders. This was further confirmed when it became possible to reproduce the high nucleation density on the substrate while covering the diamond-coated holder boundaries with a fresh Mo-foil. This phenomenon can be understood when considering the fact that the boundaries of a fresh holder gets coated simultaneously with diamond during the deposition on substrates in the first few runs. Once there is a diamond layer on the boundaries of the holder, the field strength differs at the boundaries of the holder and at the substrate. The effect is so pronounced that even 5 mm wide boundaries of the Mo holder, unintentionally coated with diamond, can reduce the energy and density of positive ions on the 3 X 3 cm(2) substrate lying on it. This, in turn, results in no nucleation on the substrate.