Can Code Become Stronger Than Isshiki Otsutsuki? well, the answer is yes however there is a but to it. So, to answers this question as clearly and accurately as possible, we have to look at chapter 56 in the Boruto manga.
So, in chapter 55 of Boruto anime, Amado stated that code has a similar karma seal/mark like Kawaki. However, Code Karma seal is not a perfect vessel nonetheless Code’s abilities surpass even Jigen’s to where they had to put limiters on Code.
So by that statement alone from Amado, we have a clear understanding of why Code could be way more powerful than Jigen. Without the limiters and only using his karma seal we know that Code could defeat Jigen to a full extent.

However, could Code match up to or become more powerful than Isshiki Otsutsuki? Nope. The reason why Code could not be on Isshiki’s level is because of a few things. Let’s go back to the fact that when Jigen fought Naruto and Sasuke while defeating both of them he was getting all heated and Jigen tried to use his full power and he could not handle Ishiki’s full power.
that’s one reason, after the fight, Jigen needed some time to recover because Ishikki’s power was too much to handle. That is reason two. Nonetheless, let’s keep him mind that Jigen is in the same category as Code as Code is an imperfect vessel, however, someone like Code has more abilities than Jigen.
Can Code Become More Powerful Than Isshiki?
It is a known fact that Code can become somewhat more powerful than Ishikki. Isshiki in the final moments confesses to Code that he must carry out his will and feed Boruto and others to the Ten tails.
Isshiki was resurrected but has a time limit to get things done. However, Kanshi Koji was the first to stand in his way. They both fought and Kanshi Koji saw that he didn’t have any chance against someone Isshiki as strong as Isshikki. Issihiki was able to use his shrinking power to a new extent that Jigen could not use. This was because of Isshiki’s shrinking abilities.
Everything in his surrounding or the space they are fighting in seconds he could shrink himself it was nothing. Also, Amado stated that if Ishikki was to unleash his full power, the planet would have been destroyed, and ain’t no doubt it could. Personally, we don’t know yet what is code full power and feats or what he is truly capable of so far. However, we can catch more details in the next chapters to come.
Final Thoughts
All of the people would disagree and said Code could not become stronger than Isshiki Otsutsuki because if Code was to become as strong as Isshiki, Isshiki would have looked for ways to make him a sacrifice with his Jigen vessel instead of keeping him. This is true. And by all means, he was once betrayed.
He even had Eida to be killed, but she was saved anyhow after all her ability allows her to use Nonotsutsuki members as she desires. This was done to use her powers to gain accurate information of events to his advantage.