His win came just a day after a former NBC president made an unsuccessful last-minute attempt to stop the convention's election. The Rev Henry J Lyons, whose presidency more than a decade ago ended with a five and a half year prison sentence for racketeering and grand theft, filed a lawsuit in a Washington DC federal court earlier this week questioning the denomination's election process.
Lyons was one of two candidates vying for the top post of one of the largest religious organisations among African Americans and the second largest Baptist denomination in the world. His bid for re-election drew some support from those who were convinced he was a changed man but many were unwilling to place him back in the leadership post after his scandal dealt a devastating blow to the denomination.
Lyons had been accused of spending church money on expensive jewellery, a Mercedes-Benz and a $700,000 home bought with a woman who is not his wife.
He challenged the denomination's new voting process and claimed it unfairly favoured his opponent, Scruggs of Alabama.
But on Wednesday, Judge Jeanette Clark denied Lyons' motion for a temporary restraining order, saying that Lyons sat and waited until the last minute to file a lawsuit rather than going to the denomination and complaining about the contested new procedures when he first came to know of them in September 2006.
Following the ruling, Lyons said he will weigh his options about whether to continue his legal fight.
Some in the convention expressed concerns that the election would splinter the denomination. But Scruggs, who served as vice president-at-large, said the overwhelming vote on Thursday "says a lot about where the convention stands in terms of its positive thrust for our future", according to The Associated Press.
The National Baptist Convention, which has a membership of over 8.3 million, held its annual session on September 7 to 11 in Memphis, Tennessee. Scruggs succeeds Dr William J Shaw, who led the convention since 1999.