Dear Barnali,
Would have been better had you gone through the definition of the term "industry" defined u/s 2(j) of the ID Act, 1947 beforehand. Profit is not the criterion for defining any industry as such : but it is the systematic co-operation between the employer and the employees so as to serve or satisfy any human need or want. Therefore, every person employed on salary or wages in a non-profit organization would be entitled to the employment benefits under the labor laws applicable to such organization subject to the parameters of eligibility.
If you were the CEO or the HR Manager of the organization, it is important that you should have at least the rudimentary knowledge of the labor laws like the ECA,1923, PWA,1936, IDA,1947, MWA,1948, State S&EA, ESIA,1948, EPFA, 1952, PBA,1965, PGA,1972, ERA,1976, SHWW(PP&R)A, 2013 etc. For instance, the Payment of Bonus Act, 1965 totally exempts the employees of institutions including hospitals, chambers of commerce and social welfare institutions established not for purposes of profit.
So, I would suggest to you to browse these laws first.