How did the Prophet, sallallaahu ‘alayhi wa sallam, die poisoned while Allaah Says (what means): {And Allaah Will Protect you from people.} [Quran 5:67]
May Allaah Bless you.

All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.

Because of the tense animosity of the disbelievers towards the Messenger of Allaah, sallallaahu ‘alayhi wa sallam, their large number, power and keenness to kill him by any means; he assigned guards, at the beginning, to protect him since it is the custom and normal reaction of human beings. When Allaah The Almighty Revealed the verse (which means): {And Allaah Will Protect you from people.} [Quran 5:67], he no longer took guards. No enemy could kill, take him captive or subjugate him. There are many examples that support this fact; such as, the attempts which were done by ‘Umayr ibn Wahb, Safwaan ibn Umayyah, ‘Aamir ibn At-Tufayl, Arbad ibn Qays, the Banu Qaynuqaa' and the Jewish woman’s attempt which is also cited in the books of the Sunnah and to which our questioner refers. However, Allaah Protected him from these and other murder attempts. Some people become confused before the fact that the Jews practiced sorcery against him, poisoned him and the disbelievers of the Quraysh struck his head and broke one of his front teeth. These incidents do not contradict the Protection of Allaah that he was granted. All the harms and pain that afflicted him were in order to raise his rank and reward, and to be an example for the callers to Allaah and the reforming scholars after him. Allaah Guaranteed for him safety from murder, captivity, madness and total damage, so that he could convey his message and complete the religion. However, accidental harms do not eradicate the total protection that he was granted. The Prophet, sallallaahu ‘alayhi wa sallam, did not care about these harms, but he was afraid that he would be killed before conveying the Message of his Lord. After Allaah Had Perfected His religion, Completed His Favor by the completion of His Sharee‘ah and after the followers of Islam, whom the Prophet, sallallaahu ‘alayhi wa sallam, brought up had become able to convey the religion; Allaah Caused His Prophet, sallallaahu ‘alayhi wa sallam, to die and that is His Law in His Creation. Allaah The Almighty Says (what means): {Every soul will taste death, and you will only be given your [full] compensation on the Day of Resurrection.} [Quran 3:185] When the Prophet, sallallaahu ‘alayhi wa sallam, felt that he had accomplished his task, conveyed the message, advised his Ummah and strived sincerely for the Sake of Allaah, he alluded to this fact in the Farewell Hajj before large gatherings. He pointed out the Islamic Sharee‘ah and advised them as if he was leaving them, as he said: "I may not meet you again in such a place after this year." So, his demise was not all of a sudden, because of killing or assassination, but it was a natural event because of fever and headache that resulted from many reasons, one of which was the poisoned meal that he had eaten at Khaybar. Such a meal did not affect him at that time because, after that, he led the armies, engaged in great wars, obtained victory, negotiated with the enemies, met the delegations and lived his normal life until he died naturally. As for the effect of the poison at the end of his life, it was in order to increase his degree and status and in order to gain the status of the martyrs. Therefore, there is no contradiction between the harms that afflicted the Prophet and the Protection of Allaah that he was granted.

Allaah Knows best.