My question is regarding these three verses of Quran.(3:90,9:66,16:106). Does these three verses mean that an apostate's repentance will never be accepted? Also can you please give me some evidence whether an apostate's repentance is accepted or not from Quran or sunnah?

All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.

The entry of an apostate Hellfire and abiding eternally in it is restricted to his death upon apostasy, as Allah Says (what means): {And whoever of you reverts from his religion [to disbelief] and dies while he is a disbeliever – for those, their deeds have become worthless in this world and the Hereafter, and those are the companions of the Fire, they will abide therein eternally.} [Quran 2:217]

As regards whoever repents from apostasy, then Allah accepts his repentance, forgives him, and admits him to Paradise, in the same manner that He admits all the believers to Paradise.

The evidence that Allah forgives him for his apostasy is the Saying of Allah (which means): {How shall Allah guide a people who disbelieved after their belief and had witnessed that the Messenger is true and clear signs had come to them? And Allah does not guide the wrongdoing people. Those – their recompense will be that upon them is the curse of Allah and the angels and the people, all together. Abiding eternally therein. The punishment will not be lightened for them, nor will they be reprieved. Except for those who repent after that and correct themselves. For indeed, Allah is Forgiving and Merciful.} [Quran 3:86-89]

Al-Qurtubi said in his Tafseer (interpretation of the Quran):

“Ibn ‘Abbaas said: “A man from the Ansar embraced Islam, then he apostatized and went back to Shirk. Then he regretted that, and sent to his people: ‘Ask the Messenger of Allah : ‘Is there any repentance for me?’ So, his people went to the Messenger of Allah and asked him: 'So and so regrets (what he did), and he told us to ask you if there is any repentance for him?' Thereupon, the verses in which Allah Says (what means): {How shall Allah guide a people who disbelieved after their belief …… Except for those who repent after that and correct themselves. For indeed, Allah is Forgiving and Merciful.} [Quran 3:86-89] were revealed. So, the Prophet sent to him and he accepted Islam.” [An-Nasaa-i]

As regards the verse in Soorah an-Nahl, in which Allah Says (what means): {Whoever disbelieves in Allah after his belief except for one who is forced [to renounce his religion] while his heart is secure in faith. But those who [willingly] open their breasts to disbelief, upon them is wrath from Allah, and for them is a great punishment.} [Quran 16:106], then it relates to the non-Muslim who did not repent from his disbelief. Ibn Katheer said in his Tafseer:

“Allah tells us that He is angry with them who willingly disbelieve in Him after clearly believing in Him, who open their hearts to disbelief finding peace in that, because they understood the faith, yet they still turned away from it. They will suffer severe punishment in the Hereafter, because they preferred this life to the Hereafter, and they left the faith for the sake of this world and Allah did not guide their hearts and help them to stand firm in the true religion. He put a seal on their hearts so that they would not be able to understand what is beneficial for them, and He sealed their ears and eyes so that they would not benefit from them. Their faculties did not help them at all, so they are unaware of what is going to happen to them. As for His Saying (which means): {… except for one who is forced [to renounce his religion] while his heart is secure in faith.}; this is an exception in the case of one who utters statements of disbelief and verbally agrees with the polytheists because he is forced to do so by the beatings and abuse to which he is subjected, but his heart refuses to accept what he is saying, and he is, in reality, at peace with his faith in Allah and His Messenger.” [End of quote]

The same applies to the verse in Soorah Al-Imran in which Allah Says (what means): {Indeed, those who reject the message after their belief and then increase in disbelief - never will their [claimed] repentance be accepted, and they are the ones astray.} [Quran 3:90]; it applies to the apostate who did not repent from his apostasy. As-Sa’di, said in his Tafseer:

“Here Allah tells us that whoever disbelieves after having believed, then increases in disbelief by persisting in wrongdoing and misguidance, and persisting in turning away from the path of guidance, his repentance will not be accepted. In other words, they will not be helped to repent in any acceptable manner; rather Allah will let them get carried away in their misguidance. It is for this reason that Allah restricted misguidance to this category of people and Says (what means): {…and they are the ones astray}; that’s to say, a misguidance that is greater than the misguidance of those who abandoned the path with insight, and if these infidels persist in their disbelief until death, then they will definitely be in perdition and eternal misery and nothing will benefit them.” [End of quote]

With regard to the verse in Soorah at-Tawbah, in which Allah Says (what means): {Make no excuse; you have disbelieved after your belief. If We pardon one faction of you - We will punish another faction because they were criminals.} [Quran 9:66]; it applies to the hypocrites who died on hypocrisy and did not repent. An-Nasafi said in its Tafseer:

“{Make no excuse}, means do not be preoccupied by your false excuses, as it will not help you after your secrets have been divulged; {you have disbelieved}; i.e. you have manifested your disbelief by your mockery {after your belief} after you have demonstrated belief; {If We pardon one faction of you}, because of their repentance and having sincere faith after hypocrisy {We will punish another faction because they were criminals.}, insisting on hypocrisy, not repenting of it.” [End of quote]

Allah knows best.