The aim of the article is to define the influence of product, process and organizational innovations on the change of fixed and variable costs and on the effectiveness of manufacturing company functioning. The article will be a comparative study. Main research tools used: observation and case study analysis. The most significant analysis areas are considerations of autonomy of efficiency of a single innovative project and its influence on fixed and variable costs. In this area, the article suggests evaluative procedure with the use of profitability threshold and sensitivity analysis.