Most probably Schopenhauer fell for believing a rumour at the time, which was likely based on a very old and travelling 'legend of war'.

The use of poison during the Peninsular War may have been a real and notorious event.

But that "a bishop" poisoned and thus harmed himself while also supposedly killing several French officers, generals no less, should have left much more traces. So many traces that we should be able to find some of them in more than fictionalised novels written much later.

That bishops in the peninsular war distinguished themselves as patriotic warriors is established: Bishop António de São José de Castro, O. Cart. is noted for action in events around Porto and Braga:

Antonio de Castro, the Bishop of Porto was a true Portuguese patriot. He had been appointed to the Portuguese Regency by Hew Whitefoord Dalrymple, but rather than work with his colleagues in Lisbon, he returned to Porto and assumed almost dictatorial powers. He called up large numbers of ordenanza which he could neither arm properly nor keep under control. The British government sent Baron Christian Adolph Friedrich von Eben and Friedrich von der Decken as military advisers. Robert Wilson also arrived in Porto and organized the Loyal Lusitanian Legion. However, Wilson soon deduced that the bishop wanted to use his new unit as a personal bodyguard. Therefore, Wilson and nearly 1,500 troops of the 1st Battalion marched to defend the frontier fortress of Almeida, leaving Eben to take command of the 2nd Battalion. In the face of Soult's invasion, the bishop kept most of the troops to defend Porto. When Freire begged for help, the bishop only sent Eben and his battalion to Braga.

The footnote line itself in question from Schopenhauer is left uncommented in Schopenhauer's Collected Works, Critical Edition.

Perhaps noteworthy to add that Schopenhauer presents the footnote in question as a commentary to:

We sometimes see a man so deeply outraged by a great wrong which he has experienced, perhaps only as a witness, that he stakes his own life, with deliberation and without salvation, on taking revenge on the perpetrator of that outrage. We see him seek out a powerful oppressor for years, finally murder him and then die himself on the scaffold, as he had foreseen and often did not even try to avoid, since his life had only retained value for him as a means of revenge. - Especially among the Spaniards such examples* can be found.

— translated from the version at gutenberg.org. The footnote commentary is completed with: "Auch findet man Beispiele im Montaigne [Les essais], Buch 2, Kap. 12."

The first line in the footnote mentions 'a certain Spanish bishop' as an example for 'willing to die out of revenge', gives no real source for it, and then continues in the next sentence with a seemingly much more precise reference. But not only can Montaigne not inform us events about 'the recent war', also the reference itself seems to confuse chapter 11 ('On cruelty') with chapter 12 ('An apology for Raymond Sebond')? If it is to Montaigne's longest essay, chapter 12, then we see mainly the important message:

We must not seek to die as an act of revenge, as Gobrias did when locked in close combat with a Persian nobleman: Darius arrived on the scene, sword in hand, but was afraid to strike for fear of killing him; Gobrias shouted to him to strike boldly, even if he had to run both of them through. Footnote: alluding to Herodotus, III, 73

At least some conflation and/or exaggeration seems to be going on.

One alternative explanation might be found in 'stories of war', often indistinguishable from pure propaganda or sailor's yarn.

One such alternative explanation for a very similar event during that war in Madrid is offered as:

Several Frenchmen poisoned by the wine

Murat in the meantime had left Spain. Before he had well recovered from a severe attack of the Madrid colic an intermittent fever supervened, and when that was removed he was ordered by his physicians to the warm baths of Bareges.

The Due de Rovigo, General Savary, who had acted so considerable a part in decoying Ferdinand to Bayonne, succeeded in the command.

It happened at this time that several French soldiers, after drinking wine in the public houses at Madrid, died, some almost immediately, others after a short illness, under unequivocal symptoms of poison.

Baron Larrey, who was at the head of the medical staff, acted with great prudence on this occasion. He sent for wine from different ventas, analyzed it, and detected narcotic ingredients in all ; and he ascertained upon full inquiry that these substances, of which laurel-water was one, were as commonly used to flavour and strengthen the Spanish wines, as litharge is to correct acidity in the lighter wines of France.

The natives were accustomed to it from their youth ; they frequently mixed their wine with water, and moreover the practice of smoking over their liquor tended to counteract its narcotic effects by stimulating the stomach and the intestines : it was therefore not surprising that they could drink it with safety; though it proved fatal to a few strangers. M. Larrey therefore justly concluded that there had been no intention of poisoning the French; if such a suspicion had been intimated, execrated as they knew themselves to be, the troops would readily have believed it; and a bloodier massacre than that of the 2d of May must have ensued.

— Robert Southey: "History of the Peninsular War", Volume 1, J. Murray: London, 1828, pp.398–399.

The same author details other occurrences of "use of poison" in that war, one involving a "friar":

The garrison of Almeida were not removed so easily. The Portugueze had kept up an irregular blockade of that fortress after Loison's departure ; they borrowed fire-arms from the Spaniards of Ciudad Rodrigo, and were so little scrupulous in their mode of warfare, that a friar poisoned the water of a tank at which the cattle belonging to the garrison used to drink.

— RS, vol 2, pp. 259–260.

[…] so that nothing might exist in Spain which had contributed towards its subjugation. Whenever the enemy approached a village, the inhabitants were enjoined to leave it, driving all their cattle into the mountains ; and they were commanded not to leave provision of any kind in their houses, unless it were poisoned ; to the end that either by want or by poison, the enemy, who were employed in destroying an unoffending people, might be themselves destroyed.

— RS, vol 3, pp. 65–66.

[…] but only one, Miguel Alzina by name, fell into the enemy's hand, and he was executed upon the glacis of Monjuic. The sentence charged him with having conspired to betray that fortress and the place of Barcelona to the Spaniards : this he had done, and in suffering for it, felt that he was dying a martyr to his country's cause : but he was charged also with having intended to poison the garrison ; and that any such purpose should have been sanctioned by the commander-in-chief, under whose sanction the scheme was formed, or that it should have been communicated to him, or even formed at all, is not to be believed.

— RS, vol 3, pp 262.

General doubts on the historicity of the related, but different in crucial details anecdote about the 'pharmacist as bishop' García de Paredes from Alarcon's 'El afrancesado' of 1856 — being a self-sacrificing poisoning 'hero' — can be read as characteristic for the Schopenhauer andecdote:

The story is told with a realism of detail which makes it all the more ferocious and quite characteristic of that war, whose memories still linger among the inhabitants of the countryside of Spain, after more than a hundred years. In Alarcon’s youth there doubtless existed still more such traditions than are current to-day and at first sight the story under discussion may very well belong to such traditions and floating anecdotes as are usually disseminated after a great war. For none of the events told is unlikely in itself, and similar incidents may have happened in the Peninsular War, as they are apt to happen in any war in which a civilian population is driven to despair by an invading host. On the other hand, it is well to consider that Alarcon was not a historian but a novelist and as such did not have to see himself obliged to narrate historical facts, ascertained or ascertainable by the historical method; he may have followed the precedent of Boccaccio and other illustrious short story writers, who added to the artistic beauty of their productions by localizing them in a definite place and in a definite period, usually not far remote from the author’s own time.

What puts us still more on our guard as to the historicity of the tale is the fact that an episode strikingly similar is told by an ancient writer, Appian, in his History of the Civil Wars. The episode in question is said to have happened in the civil war between Caesar and Pompey and to have occurred prior to the battle of Pharsalia.

— Alexander Haggarty Krappe: "The Source of Pedro Antonio de Alarcon's El Afrancesado", Romanic Review, Vol 16, 1925, pp. 54–56

The Appian episode seems like a perfect blueprint for the Alarcon story:

It is said that among the notable calamities of Gomphi, the bodies of twenty venerable men of the first rank were found lying on the floor in an apothecary's shop, not wounded, and with goblets near them, as though they were drunk, but that one of them was seated in a chair like a physician, and had no doubt dealt out poison to them.

— Appian: "The Civil Wars, Book II", Chapter X, v65, p. 347, transl by Horace White: "Appian's Roman History", Vol III, Loeb Classical Library, Heinemann: London, 1912.

That proud nationalist-inspired Spanish still discuss the figure as a poisoning-the-French-hero' (even equating Schopenhauer's anecdote with Alarcón's) seems a bit beyond historicity, but still educational.

Nevertheless, even before Alarcon had the chance to write down his version, a variation of the tale appears in 1829, this time in Constantinople:

"Ostergräuel in Constantinopel. (22. April 1821.)"

This was the end of the killing in the city, the slaughter at the gates, and the plundering of the Christian houses continued, just as the churches of the Greeks were razed to the ground. The murderers even forgot their own religion: they got drunk on the arak and wine that they found in the Christian houses, and thus many drank themselves to death in the house of an apothecary, for the apothecary had, before his death, taken all the wine in his cellar. all the wine in his cellar before he died.

— J. Annegarn: "Geschichte der neueren Zeit für die katholische Jugend, zweites Bändchen, vom westfälischen Frieden bis auf unsere Tage", Theissingsche Buchhandlung: Münster, 1829. p 448, translated.

As it seems, yet other spins on this tale/topic of ''heroically' poisoning French soldiers in that conflict' seem to be found in "El secreto del marqués de Valduero" by Marta Rivera de la Cruz (2008) — where a nobleman invites a lot of officers to a dish of poison dinner, going blind in the process; or in "El cuarzo rojo de Salamanca, Tusquets: Barcelona, 1993 by Luciano González Egido — where a young female baker falls in love with a French soldier, refuses to poison her goods sold to the French, and after being found out is offered her life for the exchange of the recipe for her delicious cookies… (Both episodes retold after: — Ama Kouassi: "Representación Del Tema De La Guerra De La Independencia En La Novela Histórica Española Reciente", Dissertation, Madrid, 2010.)

Since Schopenhauer was a German speaking man, some German language sources from memoirs of German speaking veterans then reveal equally similar stories of a cleric as poisoner of French soldiers, here even involving a pharmacist as well:

Here Schuhmacher and his comrade, Heinrich Sulzer, were quartered in the flat of a clergyman, who, despite the presence of French garrisons in the town, used the hospitality in an insidious attempt to poison the two Swiss under the pretence of a well-meant, warm welcome! We take from Schuhmacher's diary the record of the adventure connected with the fatal accommodation, of which his companion almost became a victim:

"He immediately asked us, according to Spanish custom, what religion we were. […]
Later on, the clergyman engaged in conversation with us again and told us, among other things, that many miracles had appeared in Spain against the French, that in many places the saints, even the Sancta Maria in several churches, had pronounced the curse on the Emperor Napoleon. The saints, even the Sancta Maria, had pronounced a curse on the Emperor Napoleon and against their new King Joseph in several churches. We could not refrain from laughing at his conversation and telling him that he should not make us believe such silly tales, since we knew very well that their miracles were only parish priests' tales and mechanical frauds, which only the ignorant and superstitious people believe, with which the Spanish monks blind their poor people and seek their own interest.

At this he seemed to fly into a rage again, and said, crying out, "O faithless, wicked spirits!" […]

Afterwards, when we made some remarks to him about the arrogance and vindictiveness of the Spanish monks, the barbaric behaviour of the Inquisition courts, about the all too exaggerated hypocrisy and intrigues of the Spanish clergy, and told him that such behaviour could not be pleasing to God and to justice-loving people, he jumped up in anger, grabbed a wooden image of the cross and smashed it, saying that we were not worthy to see such a thing.

When we got home, our pious priest seemed to be on friendly terms with us. We took every precaution, searched our bedroom, took our rifles loaded next to us in bed, as usual, and kept the light on. In the morning, when we wanted to leave, he was already in the antechamber, where he seemed to be doing his devotions. Finally, when we wanted to say goodbye to him, he presented us with a bottle of wine and said that we should drink it, that it would give us strength for the journey. My comrade poured two glasses full and drank one of them while I was still busy with an errand for departure, whereupon he told me that the wine was sweet but had an unpleasant bitterness. As I had often heard that French soldiers had been poisoned by wine here and there in this country, I did not trust the wine and wanted to ask the clergyman to drink it, but he excused himself with pious pretence that he did not drink wine before his mass. Then we wanted one of his maids to drink it, but he did not tolerate that either and said that his maids did not drink wine. I advised my comrade to take the bottle and have it examined to see if the wine was perhaps poisoned. When the priest noticed that my comrade wanted to go out with the bottle, he resisted. I held the priest back and told him that I would pay for the bottle or I would pay him for it. Then he told his maids to break the bottle. They wanted to do so, but my comrade managed to escape. Noise arose at the occasion. The riffraff gathered together. For my own safety, I left the house and went to the alley where several French soldiers were. At this time my comrade rode with the bottle to an apothecary, who examined the wine, which was found to be poisoned. The latter was frightened and immediately took the necessary means of rescue, and I reported the matter to the local commander, who immediately wanted to arrest the priest. But when they approached the house to stop the poisoner, he and his maidens brushed their way out of the back of the house through another door and escaped. This again gave us a warning not to trust the Spanish hypocrites and to beware of their wine. My comrade soon felt great pain. So he stayed there in the hospital, where he was attended to and saved by a French field doctor."

— Albert Maag: "Geschichte der Schweizertruppen im Kriege Napoleons I. in Spanien und Portugal (1807–1814)", Vol 2, Ernst Kuhn: Biel, 1893, p305–308.

Finally, an undated anecdote titled "Heroismus" from a German newspaper in 1829 about the Napoleonic War in Spain recounts an episode of 20 officers near 'Figueyras' (Figueres ?) dining at a monastery, with a prior dealing out the poison in wine again, to himself, all Frenchmen except one, and all his monks. Only one name is given, that of the surviving French officer Korff.

— Regensburger Zeitung, 11. April 1829, No 87, Weekend Supplement No 20: "Wöchentliche Unterhaltung. Beilage zur Regensburger Zeitung April 1829. (gBooks) Repeated verbatim for example in — Beiblage zum Amtsblatt des Prachiner Kreises, no 28, 15.Juli 1837, p112, gBooks.

We can be confident that this 'timeless' anecdote circulated also earlier and elsewhere. In "The Spirit of the Times" we read the same story, only now of an officer Kroff recounting this episode:

Self-devotion.
The following anecdote is related by captain Kroff, who served in Spain, in a regiment of infantry of the guard of Jerome, the ex-king of Westphalia. Fatigued and exhausted by forced marches, ther egimenent to which captain Kroff belonged arrived before the monastery of Figueras, in Spain. The colonel of the regiment a Frenchman, sent in an officer to demand of the prior the necessary refreshments for the men, as well as for the staff, consisting of about twenty officers. The prior, with some of the monks, came out to meet the general, assuring him that the in habitants of Figueras would provide for the soldiers, but that he himself would prepare a frugal meal for the staff. The prior's offer was accepted; captain Kroff received some commissions for the regiment, and about an hour afterwards it was announced to the prior that the dinner was served up in the refectory of the monastery. The general, who was aware that the French in Spain had reason to be on their guard in eating and drinking what was offered by the natives, invited the prior to dine with them; he and two other monks accepted the invitation in such a manner as to leave no doubt that he felt himself much flattered by it.

After the officers had taken their seats, the prior said grace, carved, ate of every dish first, and with his two brethren, who poured out the wine, drank plentifully with his guests. It was not til towards heend of there past that captain Kroff returned, having been detained by the commission of the general longer than he expected. During that interval he had found an opportunity to take some refreshment, and only participated in the conversation of the company, hosts as well as guests, at the monastery. The general, in particular, expressed his satisfaction to the prior, whose kind reception had surpassed all expectation.

Suddenly, however, the cheerfulness of the prior was changed into profound seriousness: he rose from his seat, thanked the company for the honour they bad done him, and concluded with asking if any of them had any affairs to settle in this world? adding with emphasis, "This, gentlemen, is the last meal you and I shall take on earth: in an hour we shall all be before the judgment-seat of God!" Cold trembling horror seized the amazed guests; for the prior and his two monks had poisoned the wine in which they had pledged the French officers; all the antidotes given by the French physicians were in vain: in less than an hour every man of them had ceased to live. There are few examples of self-devotion more striking than the above.

— "The Spirit of the Times", November 1825, gBooks

The earliest incidence for this Korff-story I could locate in a collection is from:
— "The Percy Ancedotes", ch. 'Patriotic Fanaticism', Sholto And Reuben Percy, Brothers of the Benedictine Monastery Mont Benger, T Boys: London, 1820, pp 100–102. gBooks

So far the oldest (digitised) German newspaper I could locate that has the Korff/monastery/prior poison version is "Der bayerische Volksfreund. 3. 1826 ## 20.04.1826". This version lacks precise dates for events and the usual identifying data, but it still has what later German versions of this anecdote lack/omit: a title of "Franzosenhaß" ('Hatred for the French'), and a byline that tersely explains:

Translated from Spanish papers

But the first locatable newspaper overall apparently did not report on this before 1819. And this English newspaper included the following paragraph:

• We know not whether this story is in reality one of those unquestionable facts with adding which the history of the Spanish contest abounds; but we are assured that its accuracy and truth are credited by many persons of integrity whose duties led them to be near the scene where it is laid. If true, as we have therefore reason to believe, it is one of the most extra-ordinary and memorable instances of self-devotion ever recorded.
  Ed.

— Sketches of Society: "The Literary Gazette: A Weekly Journal of Literature, Science, and the Fine Arts", No. 151. Saturday, December 11, 1819. p.796, gBooks

Taking all the hints together, the vague attributions, the changing settings and personnel, the sometimes vague, but sometimes almost overly specific details, and then some: It is just this friend-of-a-friend addendum from the 1819 Gazette that is intended to lend credibility to the story, but it also really completes the checklist for a now so called urban legend.

Conclusio

Summarising the answer to 'is Schopenhauer's anecdote based on facts':

Individual and isolated parts are, yes. In this protracted and nasty conflict some bishops were actively engaged in fighting the French, poison played a significant role in the entire conflict, first-hand accounts –whether true or at least embellished– of some clerics involved in poisoning others do exist, French soldiers and officers falling ill due to poison or suspected poison exist.
Further: a popular and roughly contemporary to Schopenhauer's writing anecdote about a prior of a monastery poisoning himself and French officers exists. In newspaper reports from the war or historical descriptions, this episode seems utterly absent.
Although this anecdote seems to lack historical evidence. There seems neither any concrete source for the Korff-monastery story, nor even any 'Korff' being in French service at all.
Neither is there any confirmation in historical accounts locatable of a bishop involved in self-harming poisoning, nor a significant loss of French officers or even generals in such an event.
The very similar 'apothecary as self-sacrificing patriotic poisoner' seems to be at the same time: an age-old wartime legend adapted from Greco-Roman sources to the peninsular conflict, becoming a popular story quite a bit after the Korff-story, much more popular in Spanish regions compared to the Korff-story much enjoyed over the decades in England and Germany.

Based on the available evidence now: Schopenhauer's anecdote sounds true, very true, but in its details isn't, when those are read together as a coherent sentence. There probably was no Spanish bishop poisoning himself and French generals at his table. But there probably was either rather exactly one such story circulating around 1819 simply used by the author, or Schopenhauer conflated bist and pieces based mainly on the most likely ahistorical Korff-story into his footnote.