How to tell them apart
The three look similar but serve entirely different roles. （の）上で means after completing a preparatory step before a decision (考えた上で決める), while 上（に） piles a second positive or negative fact on top of the first (面白い上に配役がいい). The N2 suffix 上 attaches to nouns to mean in terms of or from the viewpoint of that field (使用上の注意, 道義上). Mixing them up produces nonsense, since the first is about sequence, the second about addition, and the third about perspective.
- （の）上で Use （の）上で when an important action follows a preparatory step.
- 上（に） Use 上（に） to add a second fact that amplifies the first.
- 上 Use 上 after a noun to mean in terms of that field or viewpoint.
| Grammar point | Meaning | JLPT level |
|---|---|---|
| （の）上で no de | on top of; after doing; on paper | N3 |
| 上（に） ni | besides that; not just ~ but also | N3 |
| 上 | Viewed from the standpoint of / with respect to | N2 |
（の）上で no de
on top of; after doing; on paper
（の）上で can express a physical location, meaning on top of something, as in balancing on a ball. It also means after doing something, attaching to a ta-form verb or a noun with の, as in 調べた上で. In the pattern 書類の上では it means on paper, i.e. in documents or theory.
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私は仕事を一つ終えるごとにリストの上でチェックする。
I check off each task on my list as soon as I complete it.
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アシカは大きなボールの上でうまくバランスを取った。
The seal kept its balance well on the large ball.
上（に） ni
besides that; not just ~ but also
上（に）adds information on top of what was already stated, meaning
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有名な物理学者である上に、彼は偉大な小説家でもある。
In addition to being a famous physicist, he is a great novelist.
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明日の今ごろは太平洋の上を飛んでいることでしょう。
I will be flying over the Pacific about this time tomorrow.
上
Viewed from the standpoint of / with respect to
上 is a noun meaning the top or surface of something, used with particles like に and を to show position on or over a place. It also appears in the pattern 上に after plain-form words or na-adjectives/nouns to add information, meaning in addition to. In that additive use it often follows a noun plus の or a na-adjective stem.
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お祖母さんが座布団の上にちんまりとすわっていました。
The old woman was snugly sitting on a cushion.
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有名な物理学者である上に、彼は偉大な小説家でもある。
In addition to being a famous physicist, he is a great novelist.
（の）上で and 上（に） and 上 are JLPT N3–N2 grammar points that Japanese learners often mix up. This page compares all 3 side by side on meanings, usage and example sentences, so you can tell them apart.