In QGIS you can specify macros that will be executed on project startup.
To do so go to Project > Project Properties > Macros and enable the checkbox at the top. Then modify the openProject() function like this:
from qgis.utils import iface
The "1000" in the zoomScale() function represents your scale, in this case 1:1000. Save your additions by clicking on "Apply" and close the project properties dialog.
Since macros are turned off by default you have to turn them on first. You can find the corresponding option under Settings > "Options..." at the very bottom of the "General" tab ("Enable macros").
Finally just save your project, the zoom should be automatically adjusted to the given scale on the next project startup.