Pirates reportedly faced a number of issues during their trip to the Democratic Republic of the Congo but Lupopo, who won the tie 3-0, have denied those claims.
A club statement read: "Lupopo categorically denies the unfounded allegations of mistreatment towards our Champions League opponent.
"Following the defamatory allegations circulating in certain media outlets and on social media, Football Club Saint Eloi Lupopo wishes to firmly and categorically deny the accusations that it deliberately provided deplorable logistical conditions to the South Africans of Orlando Pirates Football Club during their recent stay in Lubumbashi.
"These accusations are completely unfounded, slanderous, and seriously undermine the reputation of our club and the values of respect and fair play that are dear to us.
"Football Club Saint Eloi Lupopo has always complied with the rules of the Confederation of African Football (CAF) and the highest standards of hospitality when hosting its opponents. As part of this Champions League match, we have implemented all necessary arrangements to ensure a professional welcome for the Orlando Pirates Football Club team, including hotel, transport and training facilities.
"The Club, in addition to deploring the malicious insinuations made to discredit a legitimate victory on the pitch, categorically denies the unfounded allegation that Orlando Pirates Football Club scored three goals that were subsequently disallowed. This information is completely false and in no way reflects the reality of the events observed on the pitch.
"We deeply regret that this false information, whose sole purpose appears to be to destabilize our club, has been relayed. The Club reserves the right to take legal action against the perpetrators of these defamatory allegations in order to protect its image and interests.
"Saint Eloi Lupopo Football Club remains focused on its sporting objectives and on preparing for its upcoming matches."