The early contributions to the endowment were managed from Mexico City, while missionaries in Baja California lived an austere life off of the stream of interest.

Poast 1741 donations took the form of livestock estates, which were arranged in a line to take primarily sheep on the hoof to Mexico City where the animals were slaughtered to provide the metropolis' citizens with meat in butcher shops; the income from the livestock estates then provided the 500 peso stipend per mission.

In 1836 Mexico passed an Act authorizing a petition to the Holy See for the creation of a bishopric in Alta California, and declaring that upon its creation, "the property belonging to the Pious Fund of the Californias shall be placed at the disposal of the new bishop and his successors, to be by them managed and employed for its objects, or others similar ones, always respecting the wishes of the founders".

Shortly after his consecration, Mexico delivered the properties of the Pious Fund to Bishop Diego, and they were held and administered by him until 1842, when General Antonio López de Santa Anna, President of Mexico, promulgated a decree repealing the above-mentioned provision of the Act of 1836, and directing that the Government should again receive charge of the fund.

The decree provided that "the public treasuries will acknowledge a debt of six percent per annum on the total proceeds of the sale", and specially pledged the revenue from tobacco for the payment of that amount "to carry on the objects to which said fund is destined".

By a convention between the United States and Mexico, concluded 4 July 1868 and proclaimed 1 February 1869, a Mexican and American Mixed Claims Commission was created to consider and adjudge the validity of claims held by citizens of either country against the government of the other which had arisen between the date of the Treaty of Guadalupe Hidalgo and the date of the convention creating the commission.

Upon the submission of the claim for decision, the Mexican and American commissioners disagreed as to its proper disposition, and it was referred to the umpire of the commission, Sir Edward Thornton, then British Ambassador to the US.

By the terms of the protocol, the Arbitral court was to decide first whether the liability of Mexico to make annual payments to the United States for the account of the Roman Catholic bishops of California had been rendered res judicata by the award of the Mixed Claim Commission, and second, if not, whether the claim of the United States, that Mexico was bound to continue such payments, was just.

On 14 October 1902, the tribunal at The Hague made an award judging that the liability of Mexico was established by the principle of res judicata, and by virtue of the arbitral sentence of Sir Edward Thornton, as umpire of the Mixed Claim Commission; that in consequence the Mexican Government was bound to pay the United States, for the use of the Roman Catholic archbishop and bishops of California the sum of $1,420,682.67, in extinguishment of the annuities which had accrued from 1869 to 1902, and was under the further obligation to pay perpetually an annuity of $43,050.99, in money having legal currency in Mexico.