A single or a few variables may not be sufficient to evaluate management practice effects in a complicated cropping system, so six plant and 13 soil variables were integrated using principal component analysis (PCA) to examine nine 4-yr organic potato rotations. The rotations were combinations of three forage levels (0, 1, and 2 yr of forages) with three soil amendments (monogastric compost, ruminant compost, and alfalfa meal). Quantities of amendments were estimated by soil test recommendations and amendment nutrient availabilities. In the 4th potato year, one half of each original plot was not amended (‘‘the 4th year unamended plots’’), while the other half received soil amendments (‘‘4th year amended plots’’). The first three principal components explained 67 and 63% of the overall variation for the 4th-yr amended and unamended plots, respectively. PCA ordination plots indicated that, overall, the type of soil amendments had larger effects on soil and plant variables, but forage frequencies were influential for the amendments showing weaker effects. PCA loading plots indicated that plant nutrient uptake and potato total tuber weight would be the best single variables for characterizing the current cropping systems. Plant variables, except for potato petiole nitrate, were closely displayed, but they were not strongly correlated with soil variables, which may reflect the high background fertility of this site. Applications of soil amendments in the 4th yr affected the relationships among variables, most notably the strength of relationships between soil pH and soil N variables. The results suggest that PCA provides an effective way to compare complex cropping systems, especially in situations with high site heterogeneity.