Yes, you can. Corporate travel setups normally let you add your own service fee on top of the supplier cost, because most agencies handling business travel earn more from the service they give than from whatever commission comes back from airlines and hotels. The fee is set up as a rule in your system rather than something your staff type in by hand, so it gets added the same way every time.
In most cases you can set a different fee arrangement for each corporate client, and vary it by what is being booked, so a flight booking, a hotel only booking and a visa or document service can each carry their own charge. The fee can usually be a fixed amount or worked out as a share of the booking value, and it shows as its own line on the invoice or the monthly statement so the company can see clearly what it is paying you for. That transparency matters when a client asks you to justify your charges at contract renewal time.
There are limits worth knowing. How freely you can collect the fee depends on your plan and on how the money actually reaches you. If the company settles with you on account or against a monthly statement, adding your fee is simple. If the traveller or the company pays by card at the time of booking, your payment provider has to allow the fee to be taken as part of that same payment, and not every provider handles it the same way. Whether a fee is given back when a trip is cancelled or changed is your own commercial decision, and it needs to be written into your agreement with the client so nobody argues about it later.
Before you start, write down the fee you want for each client and each booking type, then check your client contracts and ask your payment provider what it supports.