It is good that the question -- were African Americans free during the period of Reconstruction -- offers the qualifier that the answer need not be absolute, because the answer is not absolute. While the slaves were indeed officially freed by President Lincoln's Executive Order, the Emancipation Proclamation, the effect of which was codified by ratification of the Thirteenth Amendment to the United States Constitution ("Neither slavery nor involuntary servitude, except as a punishment for crime whereof the party shall have been duly convicted, shall exist within the United States, or any place subject to their jurisdiction"), the institution of slavery continued to exist in spirit if not in law. This mainly happened through a form of indentured servitude, in which the ability of African American families that were formerly enslaved continued to be tied to their former owners through quasi-legal but always immoral arrangements by which the former could conduct subsistence agricultural activities on land owned by the latter. These former slaves had to be able to provide for themselves and for their families, but the legacy of slavery deprived them of the means to do so. Consequently, they remained dependent upon their former owners for land upon which to farm.
In addition to those arrangements, blacks would not be completely free until the the middle of the 20th Century, with the 1954 U.S. Supreme Court decision in Brown v. Board of Education, and with passage of the Voting Rights Act of 1965, both of which were needed to eliminate once and for all the institution of racism that had, post-Civil War, enabled southern states to practice segregationist policies that effectively deprived blacks of their civil rights as American citizens. While these developments occurred well-after the period of Reconstruction had effectively ended, the racist policies and practices of the South that emerged out of its defeat in the Civil War laid the foundation for the continued deprivation of human rights for African American citizens in direct contravention to the spirit and the letter of the Constitution.