The Argentine says that his star midfielder has not one but two injuries to manage.
The highly-rated 19-year-old is suffering with knee and ankle problems, according to the Argentine coach.
Alli damaged his ankle just before last Sunday's 2-1 win over Swansea City, though he played the 90 minutes - and the final half-an-hour of the 1-0 defeat at West Ham three days later.
The youngster was back in the starting lineup for Saturday's 2-2 draw with Arsenal, in which he played the full match again, but Pochettino says he is playing through the pain barrier and warns that he is not a 'machine'.
"He is an incredible athlete, yes. But he is not a machine. He has a problem in his ankle and knee," he is quoted as saying by The Mail. "We have different plans for different players, we analyse the minutes they play and how they are.
"We are managing Alli, but not only him. We have a lot of players who are young and in their first or second season in the Premier League. It’s very tough and we spend a lot of time analysing to find information to give the best training sessions or recovery."
Losing Alli for any of Spurs' final nine Premier League games would be a huge blow for their title hopes, with the Lilywhites second in the table, five points behind Leicester City.
The England international has been exceptional in what is his first full season with the North Londoners, scoring seven times and setting up another five to establish himself as a key figure in this title push.