This research investigates the impact of various fertilization methods on the bioactive compound content and antioxidant activity of celery (Apium graveolens L.) root and leaf. Mineral fertilizer, poultry manure, cattle manure, sheep manure, supercompost, and molasses were applied. Total dry weight, phenolic and flavonoid compounds, and antioxidant activity were assessed, along with fiber, protein, fat, sugar, and starch in celery root. Principal component analysis (PCA) and cluster analysis were used to correlate production conditions with the parameters. The highest fiber and protein contents were found in mineral-fertilized roots, while total fat and sugar were highest in cattle-manure-fertilized roots, and starch was highest in supercompost-fertilized roots. Fertilization with supercompost yielded the highest total phenolic and flavonoid contents in leaves, while mineral fertilizer resulted in the highest antioxidant activity in roots. Notably, the highest dry weight in leaves and the highest total phenolic and flavonoid contents in roots were also observed with supercompost. PCA and cluster analysis demonstrated significant correlations between plant parts, i.e., the celery root and leaf samples, cultivation conditions, and the observed parameters, emphasizing the importance of selecting suitable cultivation methods to optimize celery’s nutritional properties. Also, these findings suggest that supercompost, a byproduct of breweries, could potentially replace animal-based organic fertilizers, addressing the problem of reduced availability due to declining livestock numbers.