Government securities are registered and cleared through an automated registry system—the Registry of Scripless Securities (RoSS)—administered by the Bureau of the Treasury. Trade settlements are referred to the Bangko Sentral ng Pilipinas (BSP).

The Philippine Payments and Settlements System (PhilPaSS) handles the processing and final settlement of fund transfer instructions in real time. PhilPaSS is a gross settlement system in which transfers are settled individually without netting debits against credit. As it is also a real time settlement system, PhilPaSS effects final settlement continuously rather than periodically at pre-specified times, provided that a sending bank has sufficient balances or credit. The settlement process is based on the real time transfer of funds from the BSP.

There is no central clearing system for corporate bonds. Clearing is conducted through a delivery, versus payment, system between concerned institutions. However, some recent corporate bond issues were settled through the Philippine Central Depository, which is normally used by the equities market.