Basically you are requesting (a) a Product Specification and (b) a sampling procedure for confirming finished product compliance with the product micro specification.
Some typical basic micro. possibilities are APC, E.coli, L.mono.,Salmonella although numerous others may be of interest. May depend on customer's requirements.
The labelled shelf-life usually implies that the product complies with the product specification at the end of the stated shelf life.
(b) is nominally a statistical question and will depend on yr specific requirements for the accuracy/confidence of yr end product "lot" results.
In practice the choice of micro. parameters / sampling frequency will probably depend on yr in-house micro. lab menu/capacity or if unavailable, yr financial budget. Micro can be expensive, especially for pathogens.
Micro count data is notoriously variable. Pathogen results are not predictable in advance. i suggest you initially test a few random samples of finished product to compare with spec. to see if count data (APC, E.coli) is well within spec or not and similarly for absence (nil detection) of pathogens like salmonella.
A realistic Product spec. may relate to yr Process / customer agreement. Perhaps you can detail the process ?