IOTs are usually derived from Supply and Use tables, which have an industry by commodity format. If you used these to derive your IOT, then you can use those to build your SAM, though note you need both the Supply AND Use tables for this. You end up with something that looks roughly like what you see on slide 7 here - with both commodity and activity (industry) rows and commodity and activity columns in your SAM. If you have the data to support it, this is probably the preferred way to go about structuring a SAM.
However, if you only have an industry by industry IOT, you can still build a SAM from that (with additional data from the country's National Accounts or another source), and this approach is far from uncommon. Instead of having separate activity and commodity rows and columns, you'll only have activity rows and columns, but you can still construct a SAM (though you may have to combine some of the non-IOT cells in your SAM to get the structure to work). As an example to hand, here is a paper outlining the construction of a SAM for Scotland using an industry by industry format (as Scotland is a part of the UK, it also shows an approach to constructing a SAM using estimates when full National Accounts data outside the IOT are not available).