Should I calculate CO2 emissions per turnover or per employee

Both, because it is not a choice but two separate fields

The answer is: neither replaces the other, the VSME baseline module asks for the absolute emissions in tonnes CO2 equivalent and for those emissions expressed per turnover unit, and sometimes also per fte. These are three different numbers that come from the same underlying data, not three ways of saying the same thing. Anyone who only enters the total misses the field that the client often wants to use precisely to compare companies of different sizes.

The calculation itself is straightforward once you have the building blocks: total emissions (scope 1, 2 and where applicable scope 3) divided by annual turnover, and if requested also divided by the average number of fte. The point where it often goes wrong is not the division but the numerator — an incomplete scope 2 or a forgotten direct emissions of greenhouse gases distorts both ratios at once. Therefore first check whether the scope breakdown is complete, including the part that is most often omitted: emissions in the value chain, before you enter the intensity figures.

Where that is stated in the VSME base module

The VSME baseline module of EFRAG explicitly distinguishes absolute emissions per scope, classified according to the scope 1/2/3 definition of the GHG Protocol, from the derived intensity measures per turnover and per employee. Both are part of the climate component of the baseline module; which of the two intensity measures a specific questionnaire requests varies per portal and is usually indicated with a separate field name. If a client only asks for one of the two, that is a choice of that portal, not an exception to the standard.