After the Battle of the Trench in 627, the men of the Jewish tribe of Banu Qurayza in Medina were executed. Critics call it a massacre ordered by the Prophet Muhammad (peace and blessings be upon him) and evidence of hostility to Jews.
“Narrated Ibn `Umar: Bani An-Nadir and Bani Quraiza fought (against the Prophet violating their peace treaty), so the Prophet exiled Bani An-Nadir and allowed Bani Quraiza to remain at their places (in Medina) taking nothing from them till they fought against the Prophet again) . He then killed their men and distributed their women, children and property among the Muslims, but some of them came to the Prophet and he granted them safety, and they embraced Islam.”Sahih al-Bukhari 4028, grading: Sahih (in Sahih al-Bukhari). English translation as given on sunnah.com
Banu Qurayza had a pact with the Muslims of Medina. During the siege of Medina by a coalition of Meccan and Arab tribes (the Battle of the Trench), they broke that pact and sided with the besiegers from inside the city, a threat to the survival of the whole community. On the earlier occasion they had been left in place untouched. When the siege failed, they surrendered after a siege of their own fortress.
And He brought down those who supported them among the People of the Scripture from their fortresses and cast terror into their hearts [so that] a party [i.e., their men] you killed, and you took captive a party [i.e., the women and children].Quran 33:26, Sahih International
“The people of (Banu) Quraiza agreed to accept the verdict of Sa`d bin Mu`adh. ... Sa`d said, "Kill their (men) warriors and take their offspring as captives,”Sahih al-Bukhari 4121, grading: Sahih (in Sahih al-Bukhari). English translation as given on sunnah.com
Banu Qurayza agreed to the judgment of Sa'd ibn Mu'adh, a chief of the Aws, who had been their ally before Islam. His verdict was against the fighting men. Women and children were not executed, with one exception reported for a woman who had killed a Muslim. Those who had come over before the end, or for whom Muslims interceded, were spared, as the narration above also records. Ustadh Abdullah Anik Misra (SeekersGuidance) stresses that this was the punishment of treason in wartime, not a war on a religion, and that the captives' descendants included the noted scholar Muhammad ibn Ka'b al-Qurazi.
“Narrated Atiyyah al-Qurazi: I was among the captives of Banu Qurayzah. They (the Companions) examined us, and those who had begun to grow hair (pubes) were killed, and those who had not were not killed. I was among those who had not grown hair.”Sunan Abi Dawud 4404, grading: Sahih (Al-Albani). English translation as given on sunnah.com
The often-quoted figure of 600 to 900 men comes from Ibn Ishaq's biography, which gives "600 or 700" and adds that some put it as high as 800 or 900, without a chain of narrators for the number. The Muslim historian W. N. Arafat argued in the Journal of the Royal Asiatic Society (1976) that the large-scale killing described there was embellished, noting that Imam Malik criticized Ibn Ishaq for taking such accounts from descendants of the tribe. Barakat Ahmad argued that only some of the tribe were executed. Other historians defend the traditional account, so the scale should be treated as uncertain.
If it will make no peace with you, but will make war against you, then you shall besiege it. When Yahweh your God delivers it into your hand, you shall strike every male of it with the edge of the sword; but the women, the little ones, the livestock, and all that is in the city, even all its plunder, you shall take for plunder for yourself. You may use the plunder of your enemies, which Yahweh your God has given you.Deuteronomy 20:12-14, World English Bible (public domain)
Sa'd's verdict matched the law of war in the Torah that Banu Qurayza themselves held: when a city makes war, every male is put to the sword and the women and little ones are taken. Martin Lings and the Islamic law scholar Ahmed Al-Dawoody both point out this correspondence. Critics who call Sa'd's verdict genocide are describing the rule of Deuteronomy.
They fought against Midian, as Yahweh commanded Moses. They killed every male. Moses said to them, “Have you saved all the women alive? Now therefore kill every male among the little ones, and kill every woman who has known man by lying with him.Numbers 31:7, 15, 17, World English Bible (public domain)
In the campaign against Midian the Bible goes further: after the men were killed, Moses (peace be upon him) ordered every male child and every woman who had been with a man to be killed as well. At Qurayza boys and women were spared.
Quran quotations: Sahih International via quran.com. Hadith quotations: the English translations and gradings shown on sunnah.com. Bible quotations: World English Bible (public domain).