Short answer. Yes, but only if the contract itself assigns each property to a specific, determinate portion of the debt. Article 2089 makes pledges and mortgages indivisible by default, but it carves out an exception: when several things secure separately identified portions of the credit, paying off one portion frees the specific property answering for it.
What the law says
there being several things given in mortgage or pledge, each one of them guarantees only a determinate portion of the credit. The debtor, in this case, shall have a right to the extinguishment of the pledge or mortgage as the portion of the debt for which each thing is specially answerable is satisfied.
Civil Code, Article 2089 — Pledge and Mortgage Are Indivisible. Read the full provision →
The default rule is indivisibility
Ordinarily, a pledge or mortgage cannot be split. Even if a debt is later divided, among the debtor's heirs, for example, the security stays intact over the whole property until the entire debt is paid, and no one can demand a proportionate release for a partial payment.
Article 2089 states this indivisibility rule first, before carving out the one exception that applies to borrowers with multiple collateral items.
The exception for separately allocated collateral
The exception applies only when the loan contract itself earmarks each piece of collateral to a determinate portion of the debt, for example, one lot securing exactly 500,000 pesos of a 1.5-million loan, a second lot securing another 500,000, and so on.
If that allocation is spelled out, paying the specific amount tied to one property entitles the debtor to have that property's pledge or mortgage extinguished, even while the rest of the loan remains outstanding.
Why the allocation has to be explicit
Without a clear, determinate allocation in the contract, the general indivisibility rule controls, and a partial payment, no matter how large, does not release any of the properties pledged or mortgaged as security.
Borrowers who want the benefit of this exception should make sure the loan or security agreement states, in writing, exactly which portion of the debt each item of collateral answers for, rather than leaving the properties pledged as a single, undivided block of security.
A practical example
Picture a borrower who mortgages two lots for one loan, with the contract stating that Lot A secures the first half of the loan and Lot B the second half. Once the borrower fully pays the amount tied to Lot A, that mortgage can be cancelled even though payments on Lot B continue.
Had the contract simply mortgaged both lots for the loan as a whole, without allocating specific amounts, the borrower would have to pay the entire loan before either lot is released.