[3][4][5] WER faced several problems during its time as a chapter organisation that included difficulty in its financing efforts and in its relationship with the Wikimedia Foundation (WMF).

Its persistent financial difficulties left the organisation with debts it was unable to pay, and on 28 August 2008 Wheeler announced on the WMUK mailing list that she was planning to call an Extraordinary General Meeting to decide on a proposal to dissolve the group.

HMRC argued that WMUK's purpose of freely disseminating information through Wikipedia would not qualify as charitable unless it included teaching and education as part of its activities.

[19] The Commission registered the company as a charity in November 2011, thereby allowing it to claim the Gift Aid tax incentive from HMRC on its donations from UK taxpayers.

[22] In response to the controversy surrounding Gibraltarpedia, the Wikimedia Foundation announced that it was taking control of UK-based donations to the organisation and was appointing an independent investigator to inquire into WMUK's governance standards and processes.

[27] Wikimedia UK also operates QRpedia, which uses QR codes in museums, archives, and other venues, so that people viewing exhibits and collections can instantly see related Wikipedia content on mobile devices, in their preferred language, where available.

In July 2012, Wikipedia's Arbitration Committee ruled that they had violated policies regarding use of multiple accounts and had behaved in an uncivil manner when faced with concerns about sexually explicit material.

[34] Despite the results of the case, Wikimedia UK's board supported van Haeften remaining in their position as chair and praised their work with the group.

CEO Jon Davies subsequently announced on 2 August 2012 that van Haeften was resigning from their position as chair to avoid creating division within the organisation.

During the month of August, material about Gibraltar appeared on the front page of Wikipedia 17 times in the "Did you know..." section as a result of the work on Gibraltarpedia.

[38][39] Gibraltar's government later stated on 21 September that their contract with Bamkin did not involve him being paid for work on Wikipedia but was limited to providing advice on the QR codes and training volunteers.

Wikipedia co-founder Jimmy Wales stated on 17 September that, if the claims about paid editing were well-founded, it was inappropriate for Bamkin to sit on the board of Wikimedia UK given its charitable status.

[38][43] In a press release following his resignation, the organisation stated that it had provided minimal material support for the effort, that Bamkin had disclosed his commercial interests, and that he had not been involved in the group's decisions regarding the project.

[42] In April 2015, a WMUK employee blocked an account on English Wikipedia he claimed was associated with then Chairman of the Conservative Party Grant Shapps.

English Wikipedia's Arbitration Committee censured the editor for his actions, claiming there was "no significant evidence" linking the blocked account to Shapps.