This question is a little challenging to deal with since it is very general and doesn’t provide a lot of detail. If a specific example of God being immoral was given, we could deal with the specifics of that particular case. However, this is a question without specifics so my answer will be general as well, although providing an example may be helpful.

Typically, there are a number of ways people have attempted to demonstrate the God of the Bible is immoral. Usually the Bible is criticized in the areas in which it disagrees with the culture’s current value system. The reasons for criticism change in light of where society is at the moment. Since God and the Bible don’t always share the same value system as the culture, the areas of contrast become the areas of criticism; which is what we see today.

This being the case, the Bible is said to be anti-science, anti-women, homophobic, repressive of sexuality, favorable toward human sacrifice, in favor of genocide, pro-slavery, promoting intolerance, pro-injustice, among other charges. Largely these criticisms come from a misunderstanding of the Bible’s message and/or the historical context to which it was directed.

At this point, it is probably helpful to provide a specific example of these general ideas. One of the most common criticisms of the Bible, and God Himself, is that He commanded “genocide”. What kind of a God would command an entire group of people to be killed?

An example comes from Deuteronomy 20:16-18, “16 Only in the cities of these peoples that the LORD your God is giving you as an inheritance, you shall not leave anything that breathes. 17 But you shall utterly destroy them, the Hittite and the Amorite, the Canaanite and the Perizzite, the Hivite and the Jebusite, as the LORD your God has commanded you.” What are we to make of this? At first glance, it seems God is arbitrarily eliminating an entire population.

Here are a few important concepts to keep in mind that may change how we think about this command. First, we must notice that this is an unusual exception, in other words, God doesn’t command entire groups of people to be killed very often. It is done in extreme circumstances and God prefers a different outcome (Genesis 18:20-32). Second, God had already been patient with these groups of people for 430 years (Genesis 15:16)! He didn’t intervene to punish for a long time; God let them pursue evil for an extended period before acting. Things got really bad before God stepped in. On the other hand, God could be criticized if He didn’t intervene: why is God allowing all this evil to take place without doing anything about it? Third, each of these groups were given the chance to leave or surrender instead of dying but they refused (Deuteronomy 20:10-12). The warning came first, the punishment followed; even in punishment God was gracious.

Fourth, this is not an example of genocide because it was not based on race or ethnicity, politics, or even culture strictly speaking (one culture is not being put above another or being preserved at the expense of another). The reason for the punishment was one of wickedness or morality. These people were being punished for wrongdoing. They burned their own children alive as sacrifices, incest and bestiality were commonplace, violence glorified; these people were immovable from the evil they performed.
Later, God punished His own people for their wickedness too; God was not picking on a specific group. Wherever immoral people are found, God will deal with them appropriately. Further, if anyone in these groups turned away from their wicked ways, God would forgive and they could join God’s people (Numbers 15:14-16). It wasn’t about race, it was about being wicked and stubbornly so (Deuteronomy. 9:4-5).

There is much more that could be said about this complex issue and there are remaining questions that were not covered. However, what has been covered should be sufficient to show our perception of something in the Bible can change drastically when background information is understood. Something that initially appeared to us to be immoral, might not be immoral after being examined more closely and the overall moral equation is understood.

For more on these difficult issues I recommend Dan Kimball’s How (Not) to Read the Bible. This is a good introduction to these complex challenges for those unfamiliar with the Bible. Or, for those who want a more in-depth look, Paul Copan’s Is God a Moral Monster? can be a good choice.