There is a yes and no answer to this question. God, as the Trinity from all eternity, is not biological in the sense of being male or female because God is spirit (John 4:24) and spirit does not have flesh and bones (Luke 24:39).1
However, in the incarnation of Christ, the second person of the Trinity, Jesus, was born a male (Luke 2:23). So, in that sense, God is made flesh (John 1:1, 14) is male in the biological sense in the person of Jesus, and He is still a man right now.
Why does the Bible refer to God in the masculine?
There is a doctrine called federal headship where the male represents the descendants. When Adam and Eve were in the Garden of Eden, Eve sinned first. But it was through Adam that sin entered the world (Romans 5:12). This demonstrates male representation. This is important because Jesus was the last Adam (1 Corinthians 15:45). He was our representative (1 Corinthians 15:22) on the cross. Furthermore, in order for Jesus to atone for our sins, He had to be born. One of the two genders had to be chosen. So, “maleness” was the chosen gender of redemption and associated with it is the characteristic of authority, federal headship, where the male represents others. So the issue of authority is associated with the male gender–due to the person of Christ. Since God is the supreme authority, it would make sense for God to refer to Himself in the male gender.
Furthermore in the revelation of the doctrine of the Trinity found in Scripture we see that there are the Father, the Son, and the Holy Spirit. Jesus is called the Son; the Word made flesh (John 1:1, 14). This demonstrates a relationship. After all, a Son has a Father. Because Jesus was made under the law (Galatians 4:4), He had to fulfill the law as a human being. It was as a male that He fulfilled the law, and since He is God in flesh and was male in the biological sense, it makes sense to conclude that the word would also be the eternal son.
