Comstock aroused intense loathing from early civil liberties groups and intense support from church based groups worried about public morals. He was a savvy political insider in New York City and was made a special agent of the United States Postal Service, with police powers up to and including the right to carry a weapon. With this power he zealously prosecuted those he suspected of either public distribution of pornography or commercial fraud, his twin obsessions. His efforts to suppress public information on sex education materials and birth control are now often viewed as misguided and medically irresponsible. He was also involved in shutting down the Louisiana Lottery, the only legal lottery in the United States at the time, and notorious for corruption. Comstock is also known for his persecution of Victoria Woodhull and Tennessee Claflin, and those associated with them. The men's journal The Days Doings had popularized lewd images of the sisters for three years and was instructed by its editor (while Comstock was present) to stop producing images of "lewd character". Comstock also took legal action against the paper for advertising contraceptives. When the sisters published an expose of an adulterous affair between Reverend Henry Ward Beecher and Elizabeth Tilton, he had the sisters imprisoned under laws forbidding the use of the postal service to distribute 'obscene material'—though they were later found 'not guilty'. Less fortunate was Ida Craddock, who committed suicide on the eve of reporting to Federal prison for distributing via the U.S. Mail various sexually explicit marriage manuals she had authored. Her final work was a lengthy public suicide note specifically condemning Comstock. Comstock claimed he drove fifteen persons to suicide in his "fight for the young". He was head vice-hunter of the New York Society for the Suppression of Vice. Comstock, the self-labeled "weeder in God's garden", arrested D. M. Bennett for publishing his "An Open Letter to Jesus Christ" and later entrapped the editor for mailing a free-love pamphlet. Bennett was prosecuted, subjected to a widely publicized trial, and imprisoned in the Albany Penitentiary. He had numerous enemies, and in later years his health was affected by a severe blow to the head from an anonymous attacker. He lectured to college audiences and wrote newspaper articles to sustain his causes. Before his death, Comstock attracted the interest of a young law student, J. Edgar Hoover, interested in his causes and methods.

During his career, Comstock clashed with Emma Goldman and Margaret Sanger. In her autobiography, Goldman referred to Comstock as the leader of America's "moral eunuchs". Through his various campaigns, he destroyed 15 tons of books, 284,000 pounds of plates for printing 'objectionable' books, and nearly 4,000,000 pictures. Comstock boasted that he was responsible for 4,000 arrests and 15 suicides. A biography of Comstock written in 1927, "Anthony Comstock: Roundsman Of The Lord" by Heywood Broun and Margaret Leech of the Algonquin Round Table examines his personal history and his investigative, surveillance and law enforcement techniques.