The team finished on 7th position in their first season. The team started the 2016–17 season precariously and finished in the religation[clarification needed] zone on the half season. That's why on 12 January 2017 the team announced Radoslav Zdravkov, a Bulgarian football legend and also frequent assistant coach in the Bulgarian national team in recent age. 2 days later from Ludogorets announced that in order to get better results from second team, they would apply big changes. Radoslav Zdravkov was announced as a headcoach with Galin Ivanov and Marcelo Chagas for assistants and one other Bulgarian legend, Spas Dzhevizov, was announced as a selectionist, and will look after for youth talents from Ludogorets Academy and other academies to join the team.
On 29 March 2017 the new youth stadium, Eagles' Nest was finished and the second team would play on it. The stadium have 2,000 seats.
From the 2017–18 season Ludogorets change the politic about the second team by taking the decision to play with only youth players of the club in the Bulgarian Second League. The team started the season against Lokomotiv Sofia and beat them with 2:1 result with a team average age being 19 years.