Protoplasts are widely used to study a variety of cellular processes because they are easy to transform, manipulate and image at high resolution. Protoplasts are thought to loose their original cell identity and therefore their origin is of minor unimportance. Hence, leaf mesophyll protoplasts are generally used to study processes active in other cell-types. However, there is no consensus whether data from protoplasts hold true for cells in intact tissues. We developed a procedure to isolate protoplasts from petals and compared their features with those of leaf protoplasts and intact tissues. Petal protoplasts derived from epidermis or mesophyll can be easily distinguished by their color and accurately reproduce the cell-specific differences in gene regulation and protein sorting observed in the intact tissue. We show that protoplasts maintain the features of the original cells in the intact tissue and, depending on their origin may produce completely different results in gene expression or protein localization assays. Consequently, analyses in leaf mesophyll protoplasts of genes or proteins that are expressed in other cell-types should be interpreted with caution. We conclude that with a few simple adjustments, to distinguish different cell-types, protoplasts can provide an excellent tool to reliably analyze highly cell-specific processes.